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de Oliveira AS, Inácio MM, de Oliveira LS, Elias Moreira AL, Alves Silva GA, Silva LOS, de Oliveira MAP, Giambiagi-deMarval M, Borges CL, Soares CMDA, Parente-Rocha JA. Immunoproteomic and immunoinformatic approaches identify secreted antigens and epitopes from Staphylococcus saprophyticus. Microb Pathog 2023:106171. [PMID: 37244490 DOI: 10.1016/j.micpath.2023.106171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Urinary tract infections (UTIs) are common human infections that compromise women's health around the world, even though they can affect men and women of all ages. Bacterial species are the primary causative agents of UTIs, while Staphylococcus saprophyticus, a gram-positive bacterium, is especially important for uncomplicated infections in young women. Despite the number of antigenic proteins identified in Staphylococcus aureus and other bacteria of the genus, there is no immunoproteomic study in S. saprophyticus. In this context, since pathogenic microorganisms secrete important proteins that interact with hosts during infection, the present work aims to identify the exoantigens from S. saprophyticus ATCC 15305 by immunoproteomic and immunoinformatic approaches. We identified 32 antigens on the exoproteome of S. saprophyticus ATCC 15305 by immunoinformatic tools. By using 2D-IB immunoproteomic analysis, it was possible to identify 3 antigenic proteins: transglycosylase IsaA, enolase and the secretory antigen Q49ZL8. In addition, 5 antigenic proteins were detected by immunoprecipitation (IP) approach, where the most abundant were bifunctional autolysin and transglycosylase IsaA proteins. The transglycosylase IsaA was the only protein detected by all the tools approaches used in this study. In this work it was possible to describe a total of 36 S. saprophyticus exoantigens. Immunoinformatic analysis allowed the identification of 5 exclusive linear B cell epitopes from S. saprophyticus and 5 epitopes presenting homology with other bacteria that cause UTIs. This work describes, for the first time, the profile of exoantigens secreted by S. saprophyticus and can contribute to the identification of new diagnostic targets of UTIs, as well as to develop vaccines and immunotherapies against bacterial urinary infections.
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Affiliation(s)
- Andrea Santana de Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Moisés Morais Inácio
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Lucas Silva de Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - André Luís Elias Moreira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Guilherme Algusto Alves Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Lana O'Hara Souza Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | | | - Marcia Giambiagi-deMarval
- Laboratório de Microbiologia Molecular, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.
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2
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Han J, Poma A. Molecular Targets for Antibody-Based Anti-Biofilm Therapy in Infective Endocarditis. Polymers (Basel) 2022; 14:polym14153198. [PMID: 35956712 PMCID: PMC9370930 DOI: 10.3390/polym14153198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Infective endocarditis (IE) is a heart disease caused by the infection of heart valves, majorly caused by Staphilococcus aureus. IE is initiated by bacteria entering the blood circulation in favouring conditions (e.g., during invasive procedures). So far, the conventional antimicrobial strategies based on the usage of antibiotics remain the major intervention for treating IE. Nevertheless, the therapeutic efficacy of antibiotics in IE is limited not only by the bacterial drug resistance, but also by the formation of biofilms, which resist the penetration of antibiotics into bacterial cells. To overcome these drawbacks, the development of anti-biofilm treatments that can expose bacteria and make them more susceptible to the action of antibiotics, therefore resulting in reduced antimicrobial resistance, is urgently required. A series of anti-biofilm strategies have been developed, and this review will focus in particular on the development of anti-biofilm antibodies. Based on the results previously reported in the literature, several potential anti-biofilm targets are discussed, such as bacterial adhesins, biofilm matrix and bacterial toxins, covering their antigenic properties (with the identification of potential promising epitopes), functional mechanisms, as well as the antibodies already developed against these targets and, where feasible, their clinical translation.
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Affiliation(s)
- Jiahe Han
- UCL Institute of Cardiovascular Science, The Rayne Building, 5 University Street, London WC1E 6JF, UK
| | - Alessandro Poma
- Division of Biomaterials and Tissue Engineering, UCL Eastman Dental Institute, Royal Free Hospital, UCL Medical School, Rowland Hill Street, London NW3 2PF, UK
- Correspondence:
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3
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Ma PY, Chong CW, Than LTL, Sulong AB, Ho KL, Neela VK, Sekawi Z, Liew YK. Impact of IsaA Gene Disruption: Decreasing Staphylococcal Biofilm and Alteration of Transcriptomic and Proteomic Profiles. Microorganisms 2022; 10:microorganisms10061119. [PMID: 35744637 PMCID: PMC9229027 DOI: 10.3390/microorganisms10061119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
Staphylococcus aureus expresses diverse proteins at different stages of growth. The immunodominant staphylococcal antigen A (IsaA) is one of the proteins that is constitutively produced by S. aureus during colonisation and infection. SACOL2584 (or isaA) is the gene that encodes this protein. It has been suggested that IsaA can hydrolyse cell walls, and there is still need to study isaA gene disruption to analyse its impact on staphylococcal phenotypes and on alteration to its transcription and protein profiles. In the present study, the growth curve in RPMI medium (which mimics human plasma), autolytic activity, cell wall morphology, fibronectin and fibrinogen adhesion and biofilm formation of S. aureus SH1000 (wildtype) was compared to that of S. aureus MS001 (isaA mutant). RNA sequencing and liquid chromatography–tandem mass spectrometry were carried out on samples of both S. aureus strains taken during the exponential growth phase, followed by bioinformatics analysis. Disruption of isaA had no obvious effect on the growth curve and autolysis ability or thickness of cell walls, but this study revealed significant strength of fibronectin adherence in S. aureus MS001. In particular, the isaA mutant formed less biofilm than S. aureus SH1000. In addition, proteomics and transcriptomics showed that the adhesin/biofilm-related genes and hemolysin genes, such as sasF, sarX and hlgC, were consistently downregulated with isaA gene disruption. The majority of the upregulated genes or proteins in S. aureus MS001 were pur genes. Taken together, this study provides insight into how isaA disruption changes the expression of other genes and has implications regarding biofilm formation and biological processes.
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Affiliation(s)
- Pei Yee Ma
- School of Postgraduate Studies, International Medical University, Kuala Lumpur 57000, Malaysia;
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, Subang Jaya 47500, Malaysia;
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang 43400, Malaysia; (L.T.L.T.); (V.K.N.); (Z.S.)
| | - Anita Binti Sulong
- Department of Medical Microbiology and Immunology, Pusat Perubatan UKM, Kuala Lumpur 56000, Malaysia;
| | - Ket Li Ho
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia;
| | - Vasantha Kumari Neela
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang 43400, Malaysia; (L.T.L.T.); (V.K.N.); (Z.S.)
| | - Zamberi Sekawi
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang 43400, Malaysia; (L.T.L.T.); (V.K.N.); (Z.S.)
| | - Yun Khoon Liew
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia;
- Correspondence:
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Tsai CM, Hajam IA, Caldera JR, Liu GY. Integrating complex host-pathogen immune environments into S. aureus vaccine studies. Cell Chem Biol 2022; 29:730-740. [PMID: 35594849 DOI: 10.1016/j.chembiol.2022.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/16/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022]
Abstract
Staphylococcus aureus (SA) is a leading cause of bacterial infection and antibiotic resistance globally. Therefore, development of an effective vaccine has been a major goal of the SA field for the past decades. With the wealth of understanding of pathogenesis, the failure of all SA vaccine trials has been a surprise. We argue that experimental SA vaccines have not worked because vaccines have been studied in naive laboratory animals, whereas clinical vaccine efficacy is tested in immune environments reprogrammed by SA. Here, we review the failed SA vaccines that have seemingly defied all principles of vaccinology. We describe major SA evasion strategies and suggest that they reshape the immune environment in a way that makes vaccines prone to failures. We propose that appropriate integration of concepts of host-pathogen interaction into vaccine study designs could lead to insight critical for the development of an effective SA vaccine.
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Affiliation(s)
- Chih-Ming Tsai
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Irshad A Hajam
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - J R Caldera
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - George Y Liu
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Division of Infectious Diseases, Rady Children's Hospital, San Diego, CA 92123, USA.
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5
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Tu C, Lu H, Zhou T, Zhang W, Deng L, Cao W, Yang Z, Wang Z, Wu X, Ding J, Xu F, Gao C. Promoting the healing of infected diabetic wound by an anti-bacterial and nano-enzyme-containing hydrogel with inflammation-suppressing, ROS-scavenging, oxygen and nitric oxide-generating properties. Biomaterials 2022; 286:121597. [DOI: 10.1016/j.biomaterials.2022.121597] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/23/2022] [Accepted: 05/18/2022] [Indexed: 12/12/2022]
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Naz K, Ullah N, Naz A, Irum S, Dar HA, Zaheer T, Shahid F, Ali A. The Epidemiological and Pangenome Landscape of Staphylococcus aureus and Identification of Conserved Novel Candidate Vaccine Antigens. CURR PROTEOMICS 2022. [DOI: 10.2174/1570164618666210212122847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background and Objective:
Staphylococcus aureus (S. aureus) is a gram-positive bacterium and one of the major nosocomial pathogen. It has the ability to acquire resistance against almost all available classes of antibiotics; Methicillin-Resistant S. aureus (MRSA) is a well-known antibiotic resistance. S. aureus is a globally distributed pathogen that need in-depth epidemiological and genomic level investigation for proper treatment and prevention.
Methods:
To explore the genomic epidemiology of S. aureus in-silico Multi Locus Sequence Typing (MLST) was carried out for 355 complete genomes. Diversity within the species was investigated through pan-genome analysis and subtractive genomic approach was employed for identification of core immunogenic targets.
Results:
Epidemiological study identified 62 different sequence types (STs) of S. aureus distributed worldwide, in which ST-8, ST-5, ST-398, ST-239, and ST-30 are the most dominant STs comprising more than 50% of the isolates. The pan-genome of S. aureus is still open with 7,199 genes and there is a major contribution (80%) of MRSA strains in the S. aureus species pangenome. The core genome (2,025 genes) of S. aureus is almost stable (comprises of 72% of S. aureus genome size) while accessory and unique genes (28% of S. aureus genome size) are gradually increasing. Screening of 2,025 core genes identified putative vaccine candidates. The best scoring and dominant B-cell and T-cell epitopes were predicted out of the selected potential vaccine candidate proteins with the help of a multi-step screening procedure.
Conclusion:
We believe that the current study will provide insight into the genetic epidemiology and diversity of S. aureus and the predicted epitopes against the pathogen can be tested further for its immunological responses within the host and may provide both humoral and cellular immunity against the disease.
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Affiliation(s)
- Kanwal Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad
44000, Pakistan
| | - Nimat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad
44000, Pakistan
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Sidra Irum
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad
44000, Pakistan
| | - Hamza Arshad Dar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad
44000, Pakistan
| | - Tahreem Zaheer
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad
44000, Pakistan
| | - Fatima Shahid
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad
44000, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad
44000, Pakistan
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7
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The cell envelope of Staphylococcus aureus selectively controls the sorting of virulence factors. Nat Commun 2021; 12:6193. [PMID: 34702812 PMCID: PMC8548510 DOI: 10.1038/s41467-021-26517-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 10/05/2021] [Indexed: 11/08/2022] Open
Abstract
Staphylococcus aureus bi-component pore-forming leukocidins are secreted toxins that directly target and lyse immune cells. Intriguingly, one of the leukocidins, Leukocidin AB (LukAB), is found associated with the bacterial cell envelope in addition to secreted into the extracellular milieu. Here, we report that retention of LukAB on the bacterial cells provides S. aureus with a pre-synthesized active toxin that kills immune cells. On the bacteria, LukAB is distributed as discrete foci in two distinct compartments: membrane-proximal and surface-exposed. Through genetic screens, we show that a membrane lipid, lysyl-phosphatidylglycerol (LPG), and lipoteichoic acid (LTA) contribute to LukAB deposition and release. Furthermore, by studying non-covalently surface-bound proteins we discovered that the sorting of additional exoproteins, such as IsaB, Hel, ScaH, and Geh, are also controlled by LPG and LTA. Collectively, our study reveals a multistep secretion system that controls exoprotein storage and protein translocation across the S. aureus cell wall.
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8
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Wang M, van den Berg S, Mora Hernández Y, Visser AH, Vera Murguia E, Koedijk DGAM, Bellink C, Bruggen H, Bakker-Woudenberg IAJM, van Dijl JM, Buist G. Differential binding of human and murine IgGs to catalytic and cell wall binding domains of Staphylococcus aureus peptidoglycan hydrolases. Sci Rep 2021; 11:13865. [PMID: 34226629 PMCID: PMC8257689 DOI: 10.1038/s41598-021-93359-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/28/2021] [Indexed: 12/27/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen causing high morbidity and mortality. Since multi-drug resistant S. aureus lineages are nowadays omnipresent, alternative tools for preventive or therapeutic interventions, like immunotherapy, are urgently needed. However, there are currently no vaccines against S. aureus. Surface-exposed and secreted proteins are regarded as potential targets for immunization against S. aureus infections. Yet, many potential staphylococcal antigens of this category do not elicit protective immune responses. To obtain a better understanding of this problem, we compared the binding of serum IgGs from healthy human volunteers, highly S. aureus-colonized patients with the genetic blistering disease epidermolysis bullosa (EB), or immunized mice to the purified S. aureus peptidoglycan hydrolases Sle1, Aly and LytM and their different domains. The results show that the most abundant serum IgGs from humans and immunized mice target the cell wall-binding domain of Sle1, and the catalytic domains of Aly and LytM. Interestingly, in a murine infection model, these particular IgGs were not protective against S. aureus bacteremia. In contrast, relatively less abundant IgGs against the catalytic domain of Sle1 and the N-terminal domains of Aly and LytM were almost exclusively detected in sera from EB patients and healthy volunteers. These latter IgGs may contribute to the protection against staphylococcal infections, as previous studies suggest that serum IgGs protect EB patients against severe S. aureus infection. Together, these observations focus attention on the use of particular protein domains for vaccination to direct potentially protective immune responses towards the most promising epitopes within staphylococcal antigens.
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Affiliation(s)
- Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Sanne van den Berg
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yaremit Mora Hernández
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Aafke Hinke Visser
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Elias Vera Murguia
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Dennis G A M Koedijk
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Channah Bellink
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Hilde Bruggen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
| | - Irma A J M Bakker-Woudenberg
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands.
| | - Girbe Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, HPC EB80, P.O. box 30001, 9700 RB, Groningen, the Netherlands
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9
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Mora-Hernández Y, Vera Murguía E, Stinenbosch J, Hernández Jauregui P, van Dijl JM, Buist G. Molecular typing and antimicrobial resistance profiling of 33 mastitis-related Staphylococcus aureus isolates from cows in the Comarca Lagunera region of Mexico. Sci Rep 2021; 11:6912. [PMID: 33767356 PMCID: PMC7994548 DOI: 10.1038/s41598-021-86453-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/10/2021] [Indexed: 11/26/2022] Open
Abstract
Mastitis in cows is a major cause of economic losses and it is commonly associated with Staphylococcus aureus. Little is known about the S. aureus lineages causing mastitis in Mexican cattle. The aim of this study was to type S. aureus isolates causing mastitis in cows from the Comarca Lagunera region in Mexico in 2015-2016. Multi-locus variable number tandem repeat fingerprinting (MLVF) of 33 S. aureus isolates obtained from 210 milk samples revealed the MLVF clusters A (n = 1), B (n = 26), C (n = 5) and D (n = 1). Spa-typing showed that clusters A and B represent the spa-type t224, cluster C includes spa-types t3196 and t416, and cluster D represents spa-type t114. The different spa-types were mirrored by the masses of protein A bands as detected by Western blotting. Antimicrobial susceptibility testing showed that one isolate was susceptible to all antimicrobials tested, whereas all other strains were resistant only to benzylpenicillin. These findings show that only four S. aureus lineages, susceptible to most antimicrobials, were responsible for causing mastitis at the time of sampling. Lastly, many isolates carried the same small plasmid, designated pSAM1. The high prevalence of pSAM1 amongst the antimicrobial-susceptible isolates suggests an association with bovine colonization or mastitis rather than antimicrobial resistance.
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Affiliation(s)
- Y Mora-Hernández
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - E Vera Murguía
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - J Stinenbosch
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | | | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
| | - G Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
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10
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Fowler VG, Das AF, Lipka-Diamond J, Schuch R, Pomerantz R, Jáuregui-Peredo L, Bressler A, Evans D, Moran GJ, Rupp ME, Wise R, Corey GR, Zervos M, Douglas PS, Cassino C. Exebacase for patients with Staphylococcus aureus bloodstream infection and endocarditis. J Clin Invest 2021; 130:3750-3760. [PMID: 32271718 DOI: 10.1172/jci136577] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUNDNovel therapeutic approaches are critically needed for Staphylococcus aureus bloodstream infections (BSIs), particularly for methicillin-resistant S. aureus (MRSA). Exebacase, a first-in-class antistaphylococcal lysin, is a direct lytic agent that is rapidly bacteriolytic, eradicates biofilms, and synergizes with antibiotics.METHODSIn this superiority-design study, we randomly assigned 121 patients with S. aureus BSI/endocarditis to receive a single dose of exebacase or placebo. All patients received standard-of-care antibiotics. The primary efficacy endpoint was clinical outcome (responder rate) on day 14.RESULTSClinical responder rates on day 14 were 70.4% and 60.0% in the exebacase + antibiotics and antibiotics-alone groups, respectively (difference = 10.4, 90% CI [-6.3, 27.2], P = 0.31), and were 42.8 percentage points higher in the prespecified exploratory MRSA subgroup (74.1% vs. 31.3%, difference = 42.8, 90% CI [14.3, 71.4], ad hoc P = 0.01). Rates of adverse events (AEs) were similar in both groups. No AEs of hypersensitivity to exebacase were reported. Thirty-day all-cause mortality rates were 9.7% and 12.8% in the exebacase + antibiotics and antibiotics-alone groups, respectively, with a notable difference in MRSA patients (3.7% vs. 25.0%, difference = -21.3, 90% CI [-45.1, 2.5], ad hoc P = 0.06). Among MRSA patients in the United States, median length of stay was 4 days shorter and 30-day hospital readmission rates were 48% lower in the exebacase-treated group compared with antibiotics alone.CONCLUSIONThis study establishes proof of concept for exebacase and direct lytic agents as potential therapeutics and supports conduct of a confirmatory study focused on exebacase to treat MRSA BSIs.TRIAL REGISTRATIONClinicaltrials.gov NCT03163446.FUNDINGContraFect Corporation.
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Affiliation(s)
- Vance G Fowler
- Duke University Medical Center, Durham, North Carolina, USA.,Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Anita F Das
- AD Stat Consulting, Guerneville, California, USA
| | | | | | | | | | - Adam Bressler
- Infectious Disease Specialists of Atlanta, Georgia, USA
| | - David Evans
- The Ohio State University, Columbus, Ohio, USA
| | | | - Mark E Rupp
- University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Robert Wise
- Johns Hopkins Bayview Medical Center, Baltimore, Maryland, USA
| | - G Ralph Corey
- Duke University Medical Center, Durham, North Carolina, USA
| | | | - Pamela S Douglas
- Duke University Medical Center, Durham, North Carolina, USA.,Duke Clinical Research Institute, Durham, North Carolina, USA
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11
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Kranjec C, Morales Angeles D, Torrissen Mårli M, Fernández L, García P, Kjos M, Diep DB. Staphylococcal Biofilms: Challenges and Novel Therapeutic Perspectives. Antibiotics (Basel) 2021; 10:131. [PMID: 33573022 PMCID: PMC7911828 DOI: 10.3390/antibiotics10020131] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
Staphylococci, like Staphylococcus aureus and S. epidermidis, are common colonizers of the human microbiota. While being harmless in many cases, many virulence factors result in them being opportunistic pathogens and one of the major causes of hospital-acquired infections worldwide. One of these virulence factors is the ability to form biofilms-three-dimensional communities of microorganisms embedded in an extracellular polymeric matrix (EPS). The EPS is composed of polysaccharides, proteins and extracellular DNA, and is finely regulated in response to environmental conditions. This structured environment protects the embedded bacteria from the human immune system and decreases their susceptibility to antimicrobials, making infections caused by staphylococci particularly difficult to treat. With the rise of antibiotic-resistant staphylococci, together with difficulty in removing biofilms, there is a great need for new treatment strategies. The purpose of this review is to provide an overview of our current knowledge of the stages of biofilm development and what difficulties may arise when trying to eradicate staphylococcal biofilms. Furthermore, we look into promising targets and therapeutic methods, including bacteriocins and phage-derived antibiofilm approaches.
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Affiliation(s)
- Christian Kranjec
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Danae Morales Angeles
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Lucía Fernández
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute of Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (L.F.); (P.G.)
- DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Pilar García
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute of Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (L.F.); (P.G.)
- DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
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12
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Armentrout EI, Liu GY, Martins GA. T Cell Immunity and the Quest for Protective Vaccines against Staphylococcus aureus Infection. Microorganisms 2020; 8:microorganisms8121936. [PMID: 33291260 PMCID: PMC7762175 DOI: 10.3390/microorganisms8121936] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus is a wide-spread human pathogen, and one of the top causative agents of nosocomial infections. The prevalence of antibiotic-resistant S. aureus strains, which are associated with higher mortality and morbidity rates than antibiotic-susceptible strains, is increasing around the world. Vaccination would be an effective preventive measure against S. aureus infection, but to date, every vaccine developed has failed in clinical trials, despite inducing robust antibody responses. These results suggest that induction of humoral immunity does not suffice to confer protection against the infection. Evidence from studies in murine models and in patients with immune defects support a role of T cell-mediated immunity in protective responses against S. aureus. Here, we review the current understanding of the mechanisms underlying adaptive immunity to S. aureus infections and discuss these findings in light of the recent S. aureus vaccine trial failures. We make the case for the need to develop anti-S. aureus vaccines that can specifically elicit robust and durable protective memory T cell subsets.
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Affiliation(s)
- Erin I. Armentrout
- Lung Institute, Cedars-Sinai Medical Center (CSMC), Los Angeles, CA 90048, USA;
- Division of Pulmonary and Critical Care Medicine, CSMC, Los Angeles, CA 90048, USA
| | - George Y. Liu
- Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92161, USA;
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gislâine A. Martins
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute (IBIRI), CSMC, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Research Division of Immunology, CSMC, Los Angeles, CA 90048, USA
- Department of Medicine, Division of Gastroenterology, CSMC, Los Angeles, CA 90048, USA
- Correspondence:
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13
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Huitema L, Phillips T, Alexeev V, Tomic-Canic M, Pastar I, Igoucheva O. Intracellular escape strategies of Staphylococcus aureus in persistent cutaneous infections. Exp Dermatol 2020; 30:1428-1439. [PMID: 33179358 DOI: 10.1111/exd.14235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/19/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022]
Abstract
Pathogenic invasion of Staphylococcus aureus is a major concern in patients with chronic skin diseases like atopic dermatitis (AD), epidermolysis bullosa (EB), or chronic diabetic foot and venous leg ulcers, and can result in persistent and life-threatening chronic non-healing wounds. Staphylococcus aureus is generally recognized as extracellular pathogens. However, S. aureus can also invade, hide and persist in skin cells to contribute to wound chronicity. The intracellular life cycle of S. aureus is currently incompletely understood, although published studies indicate that its intracellular escape strategies play an important role in persistent cutaneous infections. This review provides current scientific knowledge about the intracellular life cycle of S. aureus in skin cells, which can be classified into professional and non-professional antigen-presenting cells, and its strategies to escape adaptive defense mechanisms. First, we discuss phenotypic switch of S. aureus, which affects intracellular routing and degradation. This review also evaluates potential intracellular escape mechanism of S. aureus to avoid intracellular degradation and antigen presentation, preventing an immune response. Furthermore, we discuss potential drug targets that can interfere with the intracellular life cycle of S. aureus. Taken together, this review aimed to increase scientific understanding about the intracellular life cycle of S. aureus into skin cells and its strategies to evade the host immune response, information that is crucial to reduce pathogenic invasion and life-threatening persistence of S. aureus in chronic cutaneous infections.
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Affiliation(s)
- Leonie Huitema
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Taylor Phillips
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Vitali Alexeev
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Olga Igoucheva
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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14
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Mrochen DM, Fernandes de Oliveira LM, Raafat D, Holtfreter S. Staphylococcus aureus Host Tropism and Its Implications for Murine Infection Models. Int J Mol Sci 2020; 21:E7061. [PMID: 32992784 PMCID: PMC7582387 DOI: 10.3390/ijms21197061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a pathobiont of humans as well as a multitude of animal species. The high prevalence of multi-resistant and more virulent strains of S. aureus necessitates the development of new prevention and treatment strategies for S. aureus infection. Major advances towards understanding the pathogenesis of S. aureus diseases have been made using conventional mouse models, i.e., by infecting naïve laboratory mice with human-adapted S.aureus strains. However, the failure to transfer certain results obtained in these murine systems to humans highlights the limitations of such models. Indeed, numerous S. aureus vaccine candidates showed promising results in conventional mouse models but failed to offer protection in human clinical trials. These limitations arise not only from the widely discussed physiological differences between mice and humans, but also from the lack of attention that is paid to the specific interactions of S. aureus with its respective host. For instance, animal-derived S. aureus lineages show a high degree of host tropism and carry a repertoire of host-specific virulence and immune evasion factors. Mouse-adapted S.aureus strains, humanized mice, and microbiome-optimized mice are promising approaches to overcome these limitations and could improve transferability of animal experiments to human trials in the future.
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Affiliation(s)
- Daniel M. Mrochen
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
| | - Liliane M. Fernandes de Oliveira
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
| | - Dina Raafat
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Silva Holtfreter
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
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15
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Dreisbach A, Wang M, van der Kooi-Pol MM, Reilman E, Koedijk DGAM, Mars RAT, Duipmans J, Jonkman M, Benschop JJ, Bonarius HPJ, Groen H, Hecker M, Otto A, Bäsell K, Bernhardt J, Back JW, Becher D, Buist G, van Dijl JM. Tryptic Shaving of Staphylococcus aureus Unveils Immunodominant Epitopes on the Bacterial Cell Surface. J Proteome Res 2020; 19:2997-3010. [DOI: 10.1021/acs.jproteome.0c00043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annette Dreisbach
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Magdalena M. van der Kooi-Pol
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Ewoud Reilman
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Dennis G. A. M. Koedijk
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Ruben A. T. Mars
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - José Duipmans
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Marcel Jonkman
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Joris J. Benschop
- Pepscan Therapeutics BV, P. O. Box 2098, 8203 AB Lelystad, the Netherlands
| | | | - Herman Groen
- IQ Therapeutics, Rozenburglaan 13a, 9727 DL Groningen, the Netherlands
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Andreas Otto
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Katrin Bäsell
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Jörg Bernhardt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Jaap Willem Back
- Pepscan Therapeutics BV, P. O. Box 2098, 8203 AB Lelystad, the Netherlands
| | - Dörte Becher
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, D-17489 Greifswald, Germany
| | - Girbe Buist
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P. O. Box 30001, 9700 RB Groningen, the Netherlands
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16
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A Kayvirus Distant Homolog of Staphylococcal Virulence Determinants and VISA Biomarker Is a Phage Lytic Enzyme. Viruses 2020; 12:v12030292. [PMID: 32156046 PMCID: PMC7150955 DOI: 10.3390/v12030292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 01/07/2023] Open
Abstract
Staphylococcal bacteriophages of the Kayvirus genus are candidates for therapeutic applications. One of their proteins, Tgl, is slightly similar to two staphylococcal virulence factors, secreted autolysins of lytic transglycosylase motifs IsaA and SceD. We show that Tgl is a lytic enzyme secreted by the bacterial transport system and localizes to cell peripheries like IsaA and SceD. It causes lysis of E. coli cells expressing the cloned tgl gene, but could be overproduced when depleted of signal peptide. S. aureus cells producing Tgl lysed in the presence of nisin, which mimics the action of phage holin. In vitro, Tgl protein was able to destroy S. aureus cell walls. The production of Tgl decreased S. aureus tolerance to vancomycin, unlike the production of SceD, which is associated with decreased sensitivity to vancomycin. In the genomes of kayviruses, the tgl gene is located a few genes away from the lysK gene, encoding the major endolysin. While lysK is a late phage gene, tgl can be transcribed by a host RNA polymerase, like phage early genes. Taken together, our data indicate that tgl belongs to the kayvirus lytic module and encodes an additional endolysin that can act in concert with LysK in cell lysis.
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17
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Paull ML, Johnston T, Ibsen KN, Bozekowski JD, Daugherty PS. A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes. PLoS One 2019; 14:e0217668. [PMID: 31490930 PMCID: PMC6730857 DOI: 10.1371/journal.pone.0217668] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/22/2019] [Indexed: 12/23/2022] Open
Abstract
Antibodies are essential to functional immunity, yet the epitopes targeted by antibody repertoires remain largely uncharacterized. To aid in characterization, we developed a generalizable strategy to predict antibody-binding epitopes within individual proteins and entire proteomes. Specifically, we selected antibody-binding peptides for 273 distinct sera out of a random library and identified the peptides using next-generation sequencing. To predict antibody-binding epitopes and the antigens from which these epitopes were derived, we tiled the sequences of candidate antigens into short overlapping subsequences of length k (k-mers). We used the enrichment over background of these k-mers in the antibody-binding peptide dataset to predict antibody-binding epitopes. As a positive control, we used this approach, termed K-mer Tiling of Protein Epitopes (K-TOPE), to predict epitopes targeted by monoclonal and polyclonal antibodies of well-characterized specificity, accurately recovering their known epitopes. K-TOPE characterized a commonly targeted antigen from Rhinovirus A, predicting four epitopes recognized by antibodies present in 87% of sera (n = 250). An analysis of 2,908 proteins from 400 viral taxa that infect humans predicted seven enterovirus epitopes and five Epstein-Barr virus epitopes recognized by >30% of specimens. Analysis of Staphylococcus and Streptococcus proteomes similarly predicted 22 epitopes recognized by >30% of specimens. Twelve of these common viral and bacterial epitopes agreed with previously mapped epitopes with p-values < 0.05. Additionally, we predicted 30 HSV2-specific epitopes that were 100% specific against HSV1 in novel and previously reported antigens. Experimentally validating these candidate epitopes could help identify diagnostic biomarkers, vaccine components, and therapeutic targets. The K-TOPE approach thus provides a powerful new tool to elucidate the organisms, antigens, and epitopes targeted by human antibody repertoires.
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Affiliation(s)
- Michael L. Paull
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
- * E-mail: (MLP); (PSD)
| | - Tim Johnston
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
| | - Kelly N. Ibsen
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
| | - Joel D. Bozekowski
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
- * E-mail: (MLP); (PSD)
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18
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Naz K, Naz A, Ashraf ST, Rizwan M, Ahmad J, Baumbach J, Ali A. PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. BMC Bioinformatics 2019; 20:123. [PMID: 30871454 PMCID: PMC6419457 DOI: 10.1186/s12859-019-2713-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/03/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine designing and development process. Reverse vaccinology is considered as a cost-effective and proficient approach to screen the entire pathogen genome. To look for broad-spectrum immunogenic targets and analysis of closely-related bacterial species, the assimilation of pangenome concept into reverse vaccinology approach is essential. The categories of species pangenome such as core, accessory, and unique genes sets can be analyzed for the identification of vaccine candidates through reverse vaccinology. RESULTS We have designed an integrative computational pipeline term as "PanRV" that employs both the pangenome and reverse vaccinology approaches. PanRV comprises of four functional modules including i) Pangenome Estimation Module (PGM) ii) Reverse Vaccinology Module (RVM) iii) Functional Annotation Module (FAM) and iv) Antibiotic Resistance Association Module (ARM). The pipeline is tested by using genomic data from 301 genomes of Staphylococcus aureus and the results are verified by experimentally known antigenic data. CONCLUSION The proposed pipeline has proved to be the first comprehensive automated pipeline that can precisely identify putative vaccine candidates exploiting the microbial pangenome. PanRV is a Linux based package developed in JAVA language. An executable installer is provided for ease of installation along with a user manual at https://sourceforge.net/projects/panrv2/ .
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Affiliation(s)
- Kanwal Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000 Pakistan
| | - Anam Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000 Pakistan
| | - Shifa Tariq Ashraf
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000 Pakistan
| | - Muhammad Rizwan
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Jamil Ahmad
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
- Department of Computer Science and Information Technology, University of Malakand, Chakdara, Khyber Pakhtunkhwa Pakistan
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munchen, Germany
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000 Pakistan
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19
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Busche T, Hillion M, Van Loi V, Berg D, Walther B, Semmler T, Strommenger B, Witte W, Cuny C, Mellmann A, Holmes MA, Kalinowski J, Adrian L, Bernhardt J, Antelmann H. Comparative Secretome Analyses of Human and Zoonotic Staphylococcus aureus Isolates CC8, CC22, and CC398. Mol Cell Proteomics 2018; 17:2412-2433. [PMID: 30201737 PMCID: PMC6283302 DOI: 10.1074/mcp.ra118.001036] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Indexed: 12/24/2022] Open
Abstract
The spread of methicillin-resistant Staphylococcus aureus (MRSA) in the community, hospitals and in livestock is mediated by highly diverse virulence factors that include secreted toxins, superantigens, enzymes and surface-associated adhesins allowing host adaptation and colonization. Here, we combined proteogenomics, secretome and phenotype analyses to compare the secreted virulence factors in selected S. aureus isolates of the dominant human- and livestock-associated genetic lineages CC8, CC22, and CC398. The proteogenomic comparison revealed 2181 core genes and 1306 accessory genes in 18 S. aureus isolates reflecting the high genome diversity. Using secretome analysis, we identified 869 secreted proteins with 538 commons in eight isolates of CC8, CC22, and CC398. These include 64 predicted extracellular and 37 cell surface proteins that account for 82.4% of total secretome abundance. Among the top 10 most abundantly secreted virulence factors are the major autolysins (Atl, IsaA, Sle1, SAUPAN006375000), lipases and lipoteichoic acid hydrolases (Lip, Geh, LtaS), cytolytic toxins (Hla, Hlb, PSMβ1) and proteases (SspB). The CC398 isolates showed lower secretion of cell wall proteins, but higher secretion of α- and β-hemolysins (Hla, Hlb) which correlated with an increased Agr activity and strong hemolysis. CC398 strains were further characterized by lower biofilm formation and staphyloxanthin levels because of decreased SigB activity. Overall, comparative secretome analyses revealed CC8- or CC22-specific enterotoxin and Spl protease secretion as well as Agr- and SigB-controlled differences in exotoxin and surface protein secretion between human-specific and zoonotic lineages of S. aureus.
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Affiliation(s)
- Tobias Busche
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany; Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany
| | - Mélanie Hillion
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Vu Van Loi
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany
| | - David Berg
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Birgit Walther
- Robert Koch Institute, Advanced Light and Electron Microscopy, D-13353 Berlin, Germany; Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, D-14153 Berlin, Germany
| | - Torsten Semmler
- Robert Koch Institute, Advanced Light and Electron Microscopy, D-13353 Berlin, Germany
| | | | - Wolfgang Witte
- Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Christiane Cuny
- Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, D-48149 Münster, Germany
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, D-04318 Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, D-13355 Berlin, Germany
| | - Jörg Bernhardt
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany; Institute for Microbiology, University of Greifswald, D-17489 Greifswald, Germany
| | - Haike Antelmann
- Institute for Biology-Microbiology, Freie Universität Berlin, D-14195 Berlin, Germany.
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