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Kolenda C, Bonhomme M, Medina M, Pouilly M, Rousseau C, Troesch E, Martins-Simoes P, Stegger M, Verhoeven PO, Laumay F, Laurent F. Potential of training of anti- Staphylococcus aureus therapeutic phages against Staphylococcus epidermidis multidrug-resistant isolates is restricted by inter- and intra-sequence type specificity. mSystems 2024:e0085024. [PMID: 39248470 DOI: 10.1128/msystems.00850-24] [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: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 09/10/2024] Open
Abstract
Phage therapy appears to be a promising approach to tackle multidrug-resistant bacteria, including staphylococci. However, most anti-staphylococcal phages have been characterized in Staphylococcus aureus, while a limited number of studies investigated phage activity against S. epidermidis. We studied the potential of phage training to extend the host range of two types of anti-S. aureus phages against S. epidermidis isolates. The Appelmans protocol was applied to a mixture of Kayvirus and a mixture of Silviavirus phages repeatedly exposed to seven S. epidermidis strains representative of nosocomial-associated sequence types (ST), including the world-wide disseminated ST2. We observed increased activity only for the Kayvirus mixture against two of these strains (ST2 or ST35). Phage subpopulations isolated from the training mixture using these two strains (five/strain) exhibited different evolved phenotypes, active only against their isolation strain or strains of the same ST. Of note, 16/47 ST2 strains were susceptible to one of the groups of trained phages. A comparative genomic analysis of ancestral and trained phage genomes, conducted to identify potential bacterial determinants of such specific activity, found numerous recombination events between two of the three ancestors. However, a small number of trained phage genes had nucleotide sequence modifications impacting the corresponding protein compared to ancestral phages, two to four of them per phage genome being specific of each group of phage subpopulations exhibiting different host range. The results suggest that anti-S. aureus phages can be adapted to S. epidermidis isolates but with inter- and intra-ST specificity.ImportanceS. epidermidis is increasingly recognized as a threat for public health. Its clinical importance is notably related to multidrug resistance. Phage therapy is one of the most promising alternative therapeutic strategies to antibiotics. Nonetheless, only very few phages active against this bacterial species have been described. In the present study, we showed that phage training can be used to extend the host range of polyvalent Kayvirus phages within the Staphylococcus genera to include S. epidermidis species. In the context of rapid development of phage therapy, in vitro forced adaptation of previously characterized phages could be an appealing alternative to fastidious repeated isolation of new phages to improve the therapeutic potential of a phage collection.
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Affiliation(s)
- Camille Kolenda
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Equipe StaPath, CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Mélanie Bonhomme
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Equipe StaPath, CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Mathieu Medina
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Equipe StaPath, CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Mateo Pouilly
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Clara Rousseau
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Emma Troesch
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Patricia Martins-Simoes
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Equipe StaPath, CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Marc Stegger
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Paul O Verhoeven
- GIMAP Team, CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
- Faculty of Medicine, Université Jean Monnet St-Etienne, St-Etienne, France
- Department of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
| | - Floriane Laumay
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Equipe StaPath, CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
- Faculté de Pharmacie, Université Claude Bernard Lyon 1, Lyon, France
| | - Frédéric Laurent
- Service de bactériologie, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Equipe StaPath, CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
- Faculté de Pharmacie, Université Claude Bernard Lyon 1, Lyon, France
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2
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Beck C, Krusche J, Notaro A, Walter A, Kränkel L, Vollert A, Stemmler R, Wittmann J, Schaller M, Slavetinsky C, Mayer C, De Castro C, Peschel A. Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis. mBio 2024; 15:e0199023. [PMID: 38470054 PMCID: PMC11005348 DOI: 10.1128/mbio.01990-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The species- and clone-specific susceptibility of Staphylococcus cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycosylation-dependent phage-WTA interactions in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new S. epidermidis WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as ΦE72 but enables binding of otherwise unbound podoviruses. S. epidermidis glycerolphosphate WTA was found to be modified with glucose in a tagE-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. ΦE72 transduced several other CoNS species encoding TagE homologs, suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits interspecies horizontal gene transfer. Our study unravels a crucial mechanism of phage-Staphylococcus interaction and horizontal gene transfer, and it will help in the design of anti-staphylococcal phage therapies.IMPORTANCEPhages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus Staphylococcus bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) species has remained unknown. We describe that S. epidermidis glycosylates its WTA backbone with glucose, and we identify a cluster of three genes responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus ΦE72, suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.
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Affiliation(s)
- Christian Beck
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Janes Krusche
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Anna Notaro
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | - Axel Walter
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions/Glycobiology, University of Tübingen, Tübingen, Germany
| | - Lara Kränkel
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Anneli Vollert
- Electron-Microscopy, Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Regine Stemmler
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Johannes Wittmann
- Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Martin Schaller
- Electron-Microscopy, Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Christoph Slavetinsky
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Pediatric Surgery and Urology, University Children's Hospital Tübingen, University of Tübingen, Tübingen, Germany
| | - Christoph Mayer
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions/Glycobiology, University of Tübingen, Tübingen, Germany
| | | | - Andreas Peschel
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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3
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Alsaadi SE, Lu H, Zhang M, Dykes GF, Allison HE, Horsburgh MJ. Bacteriophages from human skin infecting coagulase-negative Staphylococcus: diversity, novelty and host resistance. Sci Rep 2024; 14:8245. [PMID: 38589670 PMCID: PMC11001980 DOI: 10.1038/s41598-024-59065-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/06/2024] [Indexed: 04/10/2024] Open
Abstract
The human skin microbiome comprises diverse populations that differ temporally between body sites and individuals. The virome is a less studied component of the skin microbiome and the study of bacteriophages is required to increase knowledge of the modulation and stability of bacterial communities. Staphylococcus species are among the most abundant colonisers of skin and are associated with both health and disease yet the bacteriophages infecting the most abundant species on skin are less well studied. Here, we report the isolation and genome sequencing of 40 bacteriophages from human skin swabs that infect coagulase-negative Staphylococcus (CoNS) species, which extends our knowledge of phage diversity. Six genetic clusters of phages were identified with two clusters representing novel phages, one of which we characterise and name Alsa phage. We identified that Alsa phages have a greater ability to infect the species S. hominis that was otherwise infected less than other CoNS species by the isolated phages, indicating an undescribed barrier to phage infection that could be in part due to numerous restriction-modification systems. The extended diversity of Staphylococcus phages here enables further research to define their contribution to skin microbiome research and the mechanisms that limit phage infection.
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Affiliation(s)
- Samah E Alsaadi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Hanshuo Lu
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Minxing Zhang
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Gregory F Dykes
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Heather E Allison
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Malcolm J Horsburgh
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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4
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Withatanung P, Janesomboon S, Vanaporn M, Muangsombut V, Charoensudjai S, Baker DJ, Wuthiekanun V, Galyov EE, Clokie MRJ, Gundogdu O, Korbsrisate S. Induced Burkholderia prophages detected from the hemoculture: a biomarker for Burkholderia pseudomallei infection. Front Microbiol 2024; 15:1361121. [PMID: 38633694 PMCID: PMC11022660 DOI: 10.3389/fmicb.2024.1361121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
Bacteriophages (phages), viruses that infect bacteria, are found in abundance not only in the environment but also in the human body. The use of phages for the diagnosis of melioidosis, a tropical infectious disease caused by Burkholderia pseudomallei, is emerging as a promising novel approach, but our understanding of conditions under which Burkholderia prophages can be induced remains limited. Here, we first demonstrated the isolation of Burkholderia phages from the hemocultures of melioidosis patients. The B. pseudomallei-positive hemoculture bottles were filtered to remove bacteria, and then phages were isolated and purified by spot and double agar overlay plaque assays. Forty blood samples (hemoculture-confirmed melioidosis) were tested, and phages were found in 30% of the samples. Transmission electron microscopy and genome analysis of the isolated phages, vB_HM387 and vB_HM795, showed that both phages are Myoviruses. These two phages were stable at a pH of 5-7 and temperatures of 25-37°C, suggesting their ability to survive in human blood. The genome sizes of vB_HM387 and vB_HM795 are 36.3 and 44.0 kb, respectively. A phylogenetic analysis indicated that vB_HM387 has homologs, but vB_HM795 is a novel Myovirus, suggesting the heterogeneity of Burkholderia phages in melioidosis patients. The key finding that Burkholderia phages could be isolated from the blood of melioidosis patients highlights the potential application of phage-based assays by detecting phages in blood as a pathogen-derived biomarker of infection.
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Affiliation(s)
- Patoo Withatanung
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sujintana Janesomboon
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Muthita Vanaporn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Veerachat Muangsombut
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Dave J. Baker
- Science Operations, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Edouard E. Galyov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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5
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Beck C, Krusche J, Elsherbini AMA, Du X, Peschel A. Phage susceptibility determinants of the opportunistic pathogen Staphylococcus epidermidis. Curr Opin Microbiol 2024; 78:102434. [PMID: 38364502 DOI: 10.1016/j.mib.2024.102434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
Staphylococcus epidermidis is a common member of the human skin and nose microbiomes and a frequent cause of invasive infections. Transducing phages accomplish the horizontal transfer of resistance and virulence genes by mispackaging of mobile-genetic elements, contributing to severe, therapy-refractory S. epidermidis infections. Lytic phages on the other hand can be interesting candidates for new anti-S. epidermidis phage therapies. Despite the importance of phages, we are only beginning to unravel S. epidermidis phage interactions. Recent studies shed new light on S. epidermidis phage diversity, host range, and receptor specificities. Modulation of cell wall teichoic acids, the major phage receptor structures, along with other phage defense mechanisms, are crucial determinants for S. epidermidis susceptibility to different phage groups.
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Affiliation(s)
- Christian Beck
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Janes Krusche
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Ahmed M A Elsherbini
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Xin Du
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Andreas Peschel
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany.
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6
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Golosova NN, Matveev AL, Tikunova NV, Khlusevich YA, Kozlova YN, Morozova VV, Babkin IV, Ushakova TA, Zhirakovskaya EV, Panina EA, Ryabchikova EI, Tikunov AY. Bacteriophage vB_SepP_134 and Endolysin LysSte_134_1 as Potential Staphylococcus-Biofilm-Removing Biological Agents. Viruses 2024; 16:385. [PMID: 38543751 PMCID: PMC10975630 DOI: 10.3390/v16030385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Bacteria of the genus Staphylococcus are significant challenge for medicine, as many species are resistant to multiple antibiotics and some are even to all of the antibiotics we use. One of the approaches to developing new therapeutics to treat staphylococcal infections is the use of bacteriophages specific to these bacteria or the lytic enzymes of such bacteriophages, which are capable of hydrolyzing the cell walls of these bacteria. In this study, a new bacteriophage vB_SepP_134 (St 134) specific to Staphylococcus epidermidis was described. This podophage, with a genome of 18,275 bp, belongs to the Andhravirus genus. St 134 was able to infect various strains of 12 of the 21 tested coagulase-negative Staphylococcus species and one clinical strain from the Staphylococcus aureus complex. The genes encoding endolysin (LysSte134_1) and tail tip lysin (LysSte134_2) were identified in the St 134 genome. Both enzymes were cloned and produced in Escherichia coli cells. The endolysin LysSte134_1 demonstrated catalytic activity against peptidoglycans isolated from S. aureus, S. epidermidis, Staphylococcus haemolyticus, and Staphylococcus warneri. LysSte134_1 was active against S. aureus and S. epidermidis planktonic cells and destroyed the biofilms formed by clinical strains of S. aureus and S. epidermidis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Artem Y. Tikunov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (N.N.G.); (N.V.T.); (Y.A.K.); (Y.N.K.); (V.V.M.); (I.V.B.); (T.A.U.); (E.A.P.); (E.I.R.)
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7
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Nicholas-Haizelden K, Murphy B, Hoptroff M, Horsburgh MJ. Bioprospecting the Skin Microbiome: Advances in Therapeutics and Personal Care Products. Microorganisms 2023; 11:1899. [PMID: 37630459 PMCID: PMC10456854 DOI: 10.3390/microorganisms11081899] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Bioprospecting is the discovery and exploration of biological diversity found within organisms, genetic elements or produced compounds with prospective commercial or therapeutic applications. The human skin is an ecological niche which harbours a rich and compositional diversity microbiome stemming from the multifactorial interactions between the host and microbiota facilitated by exploitable effector compounds. Advances in the understanding of microbial colonisation mechanisms alongside species and strain interactions have revealed a novel chemical and biological understanding which displays applicative potential. Studies elucidating the organismal interfaces and concomitant understanding of the central processes of skin biology have begun to unravel a potential wealth of molecules which can exploited for their proposed functions. A variety of skin-microbiome-derived compounds display prospective therapeutic applications, ranging from antioncogenic agents relevant in skin cancer therapy to treatment strategies for antimicrobial-resistant bacterial and fungal infections. Considerable opportunities have emerged for the translation to personal care products, such as topical agents to mitigate various skin conditions such as acne and eczema. Adjacent compound developments have focused on cosmetic applications such as reducing skin ageing and its associated changes to skin properties and the microbiome. The skin microbiome contains a wealth of prospective compounds with therapeutic and commercial applications; however, considerable work is required for the translation of in vitro findings to relevant in vivo models to ensure translatability.
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Affiliation(s)
- Keir Nicholas-Haizelden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
| | - Barry Murphy
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Michael Hoptroff
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Malcolm J. Horsburgh
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
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8
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Štrancar V, Marušić M, Tušar J, Praček N, Kolenc M, Šuster K, Horvat S, Janež N, Peterka M. Isolation and in vitro characterization of novel S. epidermidis phages for therapeutic applications. Front Cell Infect Microbiol 2023; 13:1169135. [PMID: 37293203 PMCID: PMC10244729 DOI: 10.3389/fcimb.2023.1169135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
S. epidermidis is an important opportunistic pathogen causing chronic prosthetic joint infections associated with biofilm growth. Increased tolerance to antibiotic therapy often requires prolonged treatment or revision surgery. Phage therapy is currently used as compassionate use therapy and continues to be evaluated for its viability as adjunctive therapy to antibiotic treatment or as an alternative treatment for infections caused by S. epidermidis to prevent relapses. In the present study, we report the isolation and in vitro characterization of three novel lytic S. epidermidis phages. Their genome content analysis indicated the absence of antibiotic resistance genes and virulence factors. Detailed investigation of the phage preparation indicated the absence of any prophage-related contamination and demonstrated the importance of selecting appropriate hosts for phage development from the outset. The isolated phages infect a high proportion of clinically relevant S. epidermidis strains and several other coagulase-negative species growing both in planktonic culture and as a biofilm. Clinical strains differing in their biofilm phenotype and antibiotic resistance profile were selected to further identify possible mechanisms behind increased tolerance to isolated phages.
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Affiliation(s)
- Vida Štrancar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Monika Marušić
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Jasmina Tušar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Neža Praček
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Marko Kolenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Šuster
- Valdoltra Orthopaedic Hospital, Ankaran, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nika Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Matjaž Peterka
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
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Michelle JiaMin L, Mutusamy P, Karthikeyan P, Kumaresan R, Millard A, Parimannan S, Rajandas H. Genome Characterization of Enterococcus faecalis Bacteriophage EFKL. Microbiol Resour Announc 2023:e0016023. [PMID: 37133380 DOI: 10.1128/mra.00160-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
We characterized the complete genome of the lytic Enterococcus faecalis phage EFKL, which was isolated from a sewage treatment plant in Kuala Lumpur, Malaysia. The phage, which was classified in the genus Saphexavirus, has a 58,343-bp double-stranded DNA genome containing 97 protein-encoding genes and shares 80.60% nucleotide similarity with Enterococcus phage EF653P5 and Enterococcus phage EF653P3.
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Affiliation(s)
- Loh Michelle JiaMin
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Prasanna Mutusamy
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | | | | | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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10
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Chaudhary N, Singh D, Maurya RK, Mohan B, Taneja N. Complete Genome Sequence of Salmonella Phage vB_SenA_SM5, Active against Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates. Microbiol Resour Announc 2022; 11:e0030922. [PMID: 35703563 PMCID: PMC9302169 DOI: 10.1128/mra.00309-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/02/2022] [Indexed: 11/20/2022] Open
Abstract
Phage vB_SenA_SM5, active against multiple isolates of multidrug-resistant Salmonella enterica serovar Typhi, was isolated from the sewage water of a tertiary-care referral hospital in Chandigarh, India. It has a 154.4-kb-long double-stranded DNA genome, belongs to the family Ackermannviridae, and is closest to Salmonella phage Chennai, which was isolated in southern India.
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Affiliation(s)
- Naveen Chaudhary
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Dharminder Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ravi Kumar Maurya
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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11
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Kwon H, Park SY, Kim MS, Kim SG, Park SC, Kim JH. Characterization of a Lytic Bacteriophage vB_SurP-PSU3 Infecting Staphylococcus ureilyticus and Its Efficacy Against Biofilm. Front Microbiol 2022; 13:925866. [PMID: 35923398 PMCID: PMC9340203 DOI: 10.3389/fmicb.2022.925866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/23/2022] [Indexed: 01/09/2023] Open
Abstract
In response to the increasing nosocomial infections caused by antimicrobial-resistant coagulase-negative staphylococci (CoNS), bacteriophages (phages) have emerged as an alternative to antibiotics. Staphylococcus ureilyticus, one of the representative species of the CoNS, is now considered a notable pathogen that causes nosocomial bloodstream infections, and its biofilm-forming ability increases pathogenicity and resistance to antimicrobial agents. In this study, a lytic phage infecting S. ureilyticus was newly isolated from wastewater collected from a sewage treatment plant and its biological and antimicrobial characteristics are described. The isolated phage, named vB_SurP-PSU3, was morphologically similar to Podoviridae and could simultaneously lyse some S. warneri strains used in this study. The sequenced genome of the phage consisted of linear dsDNA with 18,146 bp and genome-based phylogeny revealed that vB_SurP-PSU3 belonged to the genus Andhravirus. Although its overall genomic arrangement and contents were similar to those of other members of the Andhravirus, the predicted endolysin of vB_SurP-PSU3 distinctly differed from the other members of the genus. The bacteriolytic activity of vB_SurP-PSU3 was evaluated using S. ureilyticus ATCC 49330, and the phage could efficiently inhibit the planktonic growth of the bacteria. Moreover, the anti-biofilm analysis showed that vB_SurP-PSU3 could prevent the formation of bacterial biofilm and degrade the mature biofilm in vitro. In an additional cytotoxicity assay of vB_SurP-PSU3, no significant adverse effects were observed on the tested cell. Based on these findings, the newly isolated phage vB_SurP-PSU3 could be classified as a new member of Andhravirus and could be considered an alternative potential biocontrol agent against S. ureilyticus infections and its biofilm.
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Affiliation(s)
- Hyemin Kwon
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Seon Young Park
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - Min-Soo Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Ji Hyung Kim
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam, South Korea
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Fanaei Pirlar R, Wagemans J, Ponce Benavente L, Lavigne R, Trampuz A, Gonzalez Moreno M. Novel Bacteriophage Specific against Staphylococcus epidermidis and with Antibiofilm Activity. Viruses 2022; 14:1340. [PMID: 35746811 PMCID: PMC9230115 DOI: 10.3390/v14061340] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/15/2022] [Accepted: 06/18/2022] [Indexed: 01/19/2023] Open
Abstract
Staphylococcus epidermidis has emerged as the most important pathogen in infections related to indwelling medical devices, and although these infections are not life-threatening, their frequency and the fact that they are extremely difficult to treat represent a serious burden on the public health system. Treatment is complicated by specific antibiotic resistance genes and the formation of biofilms. Hence, novel therapeutic strategies are needed to fight these infections. A novel bacteriophage CUB-EPI_14 specific to the bacterial species S. epidermidis was isolated from sewage and characterized genomically and phenotypically. Its genome contains a total of 46,098 bp and 63 predicted genes, among which some have been associated with packaging and lysis-associated proteins, structural proteins, or DNA- and metabolism-associated proteins. No lysogeny-associated proteins or known virulence proteins were identified in the phage genome. CUB-EPI_14 showed stability over a wide range of temperatures (from -20 °C to 50 °C) and pH values (pH 3-pH 12) and a narrow host range against S. epidermidis. Potent antimicrobial and antibiofilm activities were observed when the phage was tested against a highly susceptible bacterial isolate. These encouraging results open the door to new therapeutic opportunities in the fight against resilient biofilm-associated infections caused by S. epidermidis.
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Affiliation(s)
- Rima Fanaei Pirlar
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Center for Musculoskeletal Surgery, Augustenburger Platz 1, 13353 Berlin, Germany; (R.F.P.); (L.P.B.); (A.T.)
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117 Berlin, Germany
| | - Jeroen Wagemans
- KU Leuven, Department of Biosystems, Kasteelpark Arenberg 21, 3001 Leuven, Belgium; (J.W.); (R.L.)
| | - Luis Ponce Benavente
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Center for Musculoskeletal Surgery, Augustenburger Platz 1, 13353 Berlin, Germany; (R.F.P.); (L.P.B.); (A.T.)
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117 Berlin, Germany
| | - Rob Lavigne
- KU Leuven, Department of Biosystems, Kasteelpark Arenberg 21, 3001 Leuven, Belgium; (J.W.); (R.L.)
| | - Andrej Trampuz
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Center for Musculoskeletal Surgery, Augustenburger Platz 1, 13353 Berlin, Germany; (R.F.P.); (L.P.B.); (A.T.)
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117 Berlin, Germany
| | - Mercedes Gonzalez Moreno
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Center for Musculoskeletal Surgery, Augustenburger Platz 1, 13353 Berlin, Germany; (R.F.P.); (L.P.B.); (A.T.)
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117 Berlin, Germany
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13
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Hernandez Santos H, Clark J, Terwilliger A, Maresso A. Discovery of the First Lytic Staphylococcus pseudintermedius/ Staphylococcus aureus Polyvalent Bacteriophages. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:116-124. [PMID: 36157281 PMCID: PMC9248872 DOI: 10.1089/phage.2022.0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Background There are no verified lytic Staphylococcus pseudintermedius phages in the literature and few temperate phage genomes in databases. S. pseudintermedius is an opportunistic zoonotic pathogen of great importance in veterinary and human medicine. Materials and Methods We discovered phages against canine-derived S. pseudintermedius isolates by screening dog feces, hair, and skin swabs. Fourteen new phages were isolated and characterized by genomic analysis, transmission electron microscopy, and host range determination. Results Three phages-DH2, DH5, and DS10, a phage K variant-were predicted lytic by sequencing, a designation supported by mitomycin C induction. All three are S. pseudintermedius and Staphylococcus aureus polyvalent phages, with DH2 and DS10 being strong killers of both species. Conclusions We report discovery of the first verified lytic S. pseudintermedius phages and suggest dog hair as a novel reservoir. DH2, DH5, and DS10 are promising candidates toward developing an anti-Staphylococcal phage cocktail.
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Affiliation(s)
- Haroldo Hernandez Santos
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Justin Clark
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Austen Terwilliger
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
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14
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di Lorenzo R, Bernardi A, Grumetto L, Sacchi A, Avagliano C, Coppola S, de Giovanni di Santa Severina AF, Bruno C, Paparo L, Laneri S, Dini I. Phenylalanine Butyramide Is a New Cosmetic Ingredient with Soothing and Anti-Reddening Potential. Molecules 2021; 26:6611. [PMID: 34771020 PMCID: PMC8586959 DOI: 10.3390/molecules26216611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 01/11/2023] Open
Abstract
Human skin is colonized by diverse commensal microbes, making up the skin microbiota (SM), contributing to skin integrity and homeostasis. Many of the beneficial effects aroused by the SM are exerted by microbial metabolites such as short-chain fatty acids (SCFAs), including butyric acid. The SCFAs can be used in cosmetic formulations against skin diseases to protect SM by preserving and/or restoring their natural balance. Unpleasant sensorial properties and unfavorable physico-chemical properties of butyrate strongly limit its cosmetic use. In contrast, some butyrate derivatives, including phenylalanine butyramide (C13H18N2O2, FBA), a solid form of butyric acid, are odorless while retaining the pharmacokinetic properties and safety profile of butyric acid. This study assessed the FBA's permeation across the skin and its soothing and anti-reddening potential to estimate its cosmetic application. The dosage method used to estimate FBA's levels was validated to be sure of analytical results. The FBA diffusion tests were estimated in vitro using a Franz-type vertical diffusion cell. The soothing action was evaluated in vivo by Colorimeter CL400, measuring the erythema index. The results suggest that the FBA represents an innovative way to exploit the benefits of butyric acid in the cosmetic fields since it cannot reach the bloodstream, is odorless, and has a significative soothing action (decrease the erythema index -15.7% after 30', and -17.8% after 60').
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Affiliation(s)
- Ritamaria di Lorenzo
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.d.L.); (A.B.); (L.G.); (A.S.); (C.A.)
| | - Antonietta Bernardi
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.d.L.); (A.B.); (L.G.); (A.S.); (C.A.)
| | - Lucia Grumetto
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.d.L.); (A.B.); (L.G.); (A.S.); (C.A.)
| | - Antonia Sacchi
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.d.L.); (A.B.); (L.G.); (A.S.); (C.A.)
| | - Carmen Avagliano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.d.L.); (A.B.); (L.G.); (A.S.); (C.A.)
| | - Serena Coppola
- Department of Translational Medical Science, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy; (S.C.); (A.F.d.G.d.S.S.); (C.B.); (L.P.)
- ImmunoNutritionLab at the CEINGE-Biotecnologie Avanzate s.c.ar.l Research Center, University of Naples Federico II, 80131 Naples, Italy
| | - Anna Fiorenza de Giovanni di Santa Severina
- Department of Translational Medical Science, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy; (S.C.); (A.F.d.G.d.S.S.); (C.B.); (L.P.)
- ImmunoNutritionLab at the CEINGE-Biotecnologie Avanzate s.c.ar.l Research Center, University of Naples Federico II, 80131 Naples, Italy
| | - Cristina Bruno
- Department of Translational Medical Science, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy; (S.C.); (A.F.d.G.d.S.S.); (C.B.); (L.P.)
- ImmunoNutritionLab at the CEINGE-Biotecnologie Avanzate s.c.ar.l Research Center, University of Naples Federico II, 80131 Naples, Italy
| | - Lorella Paparo
- Department of Translational Medical Science, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy; (S.C.); (A.F.d.G.d.S.S.); (C.B.); (L.P.)
- ImmunoNutritionLab at the CEINGE-Biotecnologie Avanzate s.c.ar.l Research Center, University of Naples Federico II, 80131 Naples, Italy
| | - Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.d.L.); (A.B.); (L.G.); (A.S.); (C.A.)
| | - Irene Dini
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; (R.d.L.); (A.B.); (L.G.); (A.S.); (C.A.)
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