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Michels R, Papan C, Boutin S, Alhussein F, Becker SL, Nurjadi D, Last K. Clinical relevance of Staphylococcus saccharolyticus detection in human samples: a retrospective cohort study. Infection 2024:10.1007/s15010-024-02334-6. [PMID: 38963607 DOI: 10.1007/s15010-024-02334-6] [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: 02/12/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
PURPOSE To characterize the clinical relevance of S. saccharolyticus and to identify criteria to distinguish between infection and contamination. METHODS We retrospectively investigated clinical features of patients with S. saccharolyticus detection between June 2009 and July 2021. Based on six criteria, infection was considered likely for patients with a score from 3 to 6 points, infection was considered unlikely for patients with a score from 0 to 2 points. We performed group comparison and logistic regression to identify factors than are associated with likely infection. In addition, whole genome sequencing (WGS) of 22 isolates was performed. RESULTS Of 93 patients in total, 44 were assigned to the group "infection likely" and 49 to the group "infection unlikely". Multiple regression analysis revealed "maximum body temperature during hospital stay" to have the strongest predictive effect on likely infection (adjusted odds ratio 4.40, 95% confidence interval 2.07-9.23). WGS revealed two different clades. Compared to isolates from clade A, isolates from clade B were more frequently associated with implanted medical devices (3/10 vs. 9/12, p = 0.046) and a shorter time to positivity (TTP) (4.5 vs. 3, p = 0.016). Both clades did neither differ significantly in terms of causing a likely infection (clade A 7/10 vs. clade B 5/12, p = 0.23) nor in median length of hospital stay (28 vs. 15.5 days, p = 0.083) and length of stay at the ICU (21 vs. 3.5 days, p = 0.14). CONCLUSION These findings indicate that S. saccharolyticus can cause clinically relevant infections. Differentiation between infection and contamination remains challenging.
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Affiliation(s)
- Ricarda Michels
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Cihan Papan
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany.
- Institute for Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany.
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
- Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
- Airway Research Center North (ARCN), German center for Lung Research (DZL), Lübeck, Germany
| | - Farah Alhussein
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Sören L Becker
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
- Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Katharina Last
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
- Institute for Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, Bonn, Germany
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2
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Twomey E, O’Connor PM, Coffey A, Kiste M, Guinane CM, Hill C, Field D, Begley M. Inhibition of Clinical MRSA Isolates by Coagulase Negative Staphylococci of Human Origin. Antibiotics (Basel) 2024; 13:338. [PMID: 38667016 PMCID: PMC11047365 DOI: 10.3390/antibiotics13040338] [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: 03/05/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/29/2024] Open
Abstract
Staphylococcus aureus is frequently highlighted as a priority for novel drug research due to its pathogenicity and ability to develop antibiotic resistance. Coagulase-negative staphylococci (CoNS) are resident flora of the skin and nares. Previous studies have confirmed their ability to kill and prevent colonization by S. aureus through the production of bioactive substances. This study screened a bank of 37 CoNS for their ability to inhibit the growth of methicillin-resistant S. aureus (MRSA). Deferred antagonism assays, growth curves, and antibiofilm testing performed with the cell-free supernatant derived from overnight CoNS cultures indicated antimicrobial and antibiofilm effects against MRSA indicators. Whole genome sequencing and BAGEL4 analysis of 11 CoNS isolates shortlisted for the inhibitory effects they displayed against MRSA led to the identification of two strains possessing complete putative bacteriocin operons. The operons were predicted to encode a nukacin variant and a novel epilancin variant. From this point, strains Staphylococcus hominis C14 and Staphylococcus epidermidis C33 became the focus of the investigation. Through HPLC, a peptide identical to previously characterized nukacin KQU-131 and a novel epilancin variant were isolated from cultures of C14 and C33, respectively. Mass spectrometry confirmed the presence of each peptide in the active fractions. Spot-on-lawn assays demonstrated both bacteriocins could inhibit the growth of an MRSA indicator. The identification of natural products with clinically relevant activity is important in today's climate of escalating antimicrobial resistance and a depleting antibiotic pipeline. These findings also highlight the prospective role CoNS may play as a source of bioactive substances with activity against critical pathogens.
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Affiliation(s)
- Ellen Twomey
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (E.T.); (A.C.); (C.M.G.)
- APC Microbiome Ireland, University College Cork, T12 YN60 Cork, Ireland;
| | | | - Aidan Coffey
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (E.T.); (A.C.); (C.M.G.)
- APC Microbiome Ireland, University College Cork, T12 YN60 Cork, Ireland;
| | - Maija Kiste
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (E.T.); (A.C.); (C.M.G.)
| | - Caitriona M. Guinane
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (E.T.); (A.C.); (C.M.G.)
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, T12 YN60 Cork, Ireland;
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
| | - Des Field
- APC Microbiome Ireland, University College Cork, T12 YN60 Cork, Ireland;
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
| | - Máire Begley
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (E.T.); (A.C.); (C.M.G.)
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3
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Torres Salazar BO, Dema T, Schilling NA, Janek D, Bornikoel J, Berscheid A, Elsherbini AMA, Krauss S, Jaag SJ, Lämmerhofer M, Li M, Alqahtani N, Horsburgh MJ, Weber T, Beltrán-Beleña JM, Brötz-Oesterhelt H, Grond S, Krismer B, Peschel A. Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus. Nat Microbiol 2024; 9:200-213. [PMID: 38110697 DOI: 10.1038/s41564-023-01544-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
Antagonistic bacterial interactions often rely on antimicrobial bacteriocins, which attack only a narrow range of target bacteria. However, antimicrobials with broader activity may be advantageous. Here we identify an antimicrobial called epifadin, which is produced by nasal Staphylococcus epidermidis IVK83. It has an unprecedented architecture consisting of a non-ribosomally synthesized peptide, a polyketide component and a terminal modified amino acid moiety. Epifadin combines a wide antimicrobial target spectrum with a short life span of only a few hours. It is highly unstable under in vivo-like conditions, potentially as a means to limit collateral damage of bacterial mutualists. However, Staphylococcus aureus is eliminated by epifadin-producing S. epidermidis during co-cultivation in vitro and in vivo, indicating that epifadin-producing commensals could help prevent nasal S. aureus carriage. These insights into a microbiome-derived, previously unknown antimicrobial compound class suggest that limiting the half-life of an antimicrobial may help to balance its beneficial and detrimental activities.
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Affiliation(s)
- Benjamin O Torres Salazar
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Daniela Janek
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Jan Bornikoel
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Berscheid
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Ahmed M A Elsherbini
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Sophia Krauss
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Simon J Jaag
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Norah Alqahtani
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Malcolm J Horsburgh
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - José Manuel Beltrán-Beleña
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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4
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Afshar M, Møllebjerg A, Minero GA, Hollensteiner J, Poehlein A, Himmelbach A, Lange J, Meyer RL, Brüggemann H. Biofilm formation and inflammatory potential of Staphylococcus saccharolyticus: A possible cause of orthopedic implant-associated infections. Front Microbiol 2022; 13:1070201. [DOI: 10.3389/fmicb.2022.1070201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus saccharolyticus, a coagulase-negative staphylococcal species, has some unusual characteristics for human-associated staphylococci, such as slow growth and its preference for anoxic culture conditions. This species is a relatively abundant member of the human skin microbiota, but its microbiological properties, as well as the pathogenic potential, have scarcely been investigated so far, despite being occasionally isolated from different types of infections including orthopedic implant-associated infections. Here, we investigated the growth and biofilm properties of clinical isolates of S. saccharolyticus and determined host cell responses. Growth assessments in anoxic and oxic conditions revealed strain-dependent outcomes, as some strains can also grow aerobically. All tested strains of S. saccharolyticus were able to form biofilm in a microtiter plate assay. Strain-dependent differences were determined by optical coherence tomography, revealing that medium supplementation with glucose and sodium chloride enhanced biofilm formation. Visualization of the biofilm by confocal laser scanning microscopy revealed the role of extracellular DNA in the biofilm structure. In addition to attached biofilms, S. saccharolyticus also formed bacterial aggregates at an early stage of growth. Transcriptome analysis of biofilm-grown versus planktonic cells revealed a set of upregulated genes in biofilm-embedded cells, including factors involved in adhesion, colonization, and competition such as epidermin, type I toxin-antitoxin system, and phenol-soluble modulins (beta and epsilon). To investigate consequences for the host after encountering S. saccharolyticus, cytokine profiling and host cell viability were assessed by infection experiments with differentiated THP-1 cells. The microorganism strongly triggered the secretion of the tested pro-inflammatory cyto- and chemokines IL-6, IL-8, and TNF-alpha, determined at 24 h post-infection. S. saccharolyticus was less cytotoxic than Staphylococcus aureus. Taken together, the results indicate that S. saccharolyticus has substantial pathogenic potential. Thus, it can be a potential cause of orthopedic implant-associated infections and other types of deep-seated infections.
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5
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Ponraj DS, Falstie-Jensen T, Jørgensen NP, Ravn C, Brüggemann H, Lange J. Diagnosis of orthopaedic-implant-associated infections caused by slow-growing Gram-positive anaerobic bacteria - a clinical perspective. J Bone Jt Infect 2021; 6:367-378. [PMID: 34660180 PMCID: PMC8515996 DOI: 10.5194/jbji-6-367-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022] Open
Abstract
Slow-growing Gram-positive anaerobic bacteria (SGAB) such as
Cutibacterium acnes are increasingly recognized as causative agents of implant-associated infections (IAIs) in orthopaedic surgeries. SGAB IAIs are difficult to diagnose because of their non-specific clinical and laboratory findings as well as the fastidious growth conditions required by these bacteria. A high degree of clinical suspicion and awareness of the various available diagnostic methods is therefore important. This review gives an overview of the current knowledge regarding SGAB IAI, providing details about clinical features and available diagnostic methodologies. In recent years, new methods for the diagnosis of IAI were developed, but there is limited knowledge about their usefulness in SGAB IAI. Further studies are required to determine the ideal diagnostic methodology to identify these infections so that they are not overlooked and mistakenly classified as aseptic failure.
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Affiliation(s)
| | - Thomas Falstie-Jensen
- Department of Orthopaedic Surgery, Aarhus University Hospital, Aarhus, 8200, Denmark
| | | | - Christen Ravn
- Department of Orthopaedic Surgery, Lillebaelt Hospital, Kolding, 6000, Denmark
| | | | - Jeppe Lange
- Department of Clinical Medicine, Aarhus University, Aarhus, 8000, Denmark.,Department of Orthopaedic Surgery, Horsens Regional Hospital, Horsens, 8700, Denmark
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6
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Michels R, Last K, Becker SL, Papan C. Update on Coagulase-Negative Staphylococci-What the Clinician Should Know. Microorganisms 2021; 9:microorganisms9040830. [PMID: 33919781 PMCID: PMC8070739 DOI: 10.3390/microorganisms9040830] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 02/07/2023] Open
Abstract
Coagulase-negative staphylococci (CoNS) are among the most frequently recovered bacteria in routine clinical care. Their incidence has steadily increased over the past decades in parallel to the advancement in medicine, especially in regard to the utilization of foreign body devices. Many new species have been described within the past years, while clinical information to most of those species is still sparse. In addition, interspecies differences that render some species more virulent than others have to be taken into account. The distinct populations in which CoNS infections play a prominent role are preterm neonates, patients with implanted medical devices, immunodeficient patients, and those with other relevant comorbidities. Due to the property of CoNS to colonize the human skin, contamination of blood cultures or other samples occurs frequently. Hence, the main diagnostic hurdle is to correctly identify the cases in which CoNS are causative agents rather than contaminants. However, neither phenotypic nor genetic tools have been able to provide a satisfying solution to this problem. Another dilemma of CoNS in clinical practice pertains to their extensive antimicrobial resistance profile, especially in healthcare settings. Therefore, true infections caused by CoNS most often necessitate the use of second-line antimicrobial drugs.
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7
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Söderquist B, Afshar M, Poehlein A, Brüggemann H. Staphylococcus saccharolyticus Associated with Prosthetic Joint Infections: Clinical Features and Genomic Characteristics. Pathogens 2021; 10:pathogens10040397. [PMID: 33810311 PMCID: PMC8066136 DOI: 10.3390/pathogens10040397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 01/20/2023] Open
Abstract
The anaerobic coagulase-negative staphylococcal species Staphylococcus saccharolyticus is a member of the normal skin microbiota. However, S. saccharolyticus is rarely found in clinical specimens and its pathogenic potential is unclear. The clinical data of prosthetic hip (n = 5) and shoulder (n = 2) joint implant-associated infections where S. saccharolyticus was detected in periprosthetic tissue specimens are described. The prosthetic hip joint infection cases presented as “aseptic” loosening and may represent chronic, insidious, low-grade prosthetic joint infections (PJIs), eventually resulting in loosening of prosthetic components. All cases were subjected to one-stage revision surgery and the long-term outcome was good. The shoulder joint infections had an acute onset. Polymicrobial growth, in all cases with Cutibacterium acnes, was found in 4/7 patients. All but one case were treated with long-term administration of beta-lactam antibiotics. Whole-genome sequencing (WGS) of the isolates was performed and potential virulence traits were identified. WGS could distinguish two phylogenetic clades (clades 1 and 2), which likely represent distinct subspecies of S. saccharolyticus. Little strain individuality was observed among strains from the same clade. Strains of clade 2 were exclusively associated with hip PJIs, whereas clade 1 strains originated from shoulder PJIs. It is possible that strains of the two clades colonize different skin habitats. In conclusion, S. saccharolyticus has the potential to cause PJIs that were previously regarded as aseptic loosening of prosthetic joint devices.
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Affiliation(s)
- Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 701 82 Örebro, Sweden
- Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, 701 85 Örebro, Sweden
- Correspondence: ; Tel.: +46-19-6023571
| | - Mastaneh Afshar
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (M.A.); (H.B.)
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Holger Brüggemann
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (M.A.); (H.B.)
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8
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Complete Genome Sequences of Two Staphylococcus saccharolyticus Strains Isolated from Prosthetic Joint Infections. Microbiol Resour Announc 2021; 10:10/10/e00157-21. [PMID: 33707331 PMCID: PMC7953294 DOI: 10.1128/mra.00157-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus saccharolyticus is a human skin bacterium and is occasionally associated with prosthetic joint infections (PJIs). Here, we report the complete genome sequences of two strains that were isolated from shoulder and hip PJIs. The genomes show signs of reductive evolution; around 21% of all coding sequences are inactivated by frameshift mutations. Staphylococcus saccharolyticus is a human skin bacterium and is occasionally associated with prosthetic joint infections (PJIs). Here, we report the complete genome sequences of two strains that were isolated from shoulder and hip PJIs. The genomes show signs of reductive evolution; around 21% of all coding sequences are inactivated by frameshift mutations.
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9
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Stahl-Rommel S, Jain M, Nguyen HN, Arnold RR, Aunon-Chancellor SM, Sharp GM, Castro CL, John KK, Juul S, Turner DJ, Stoddart D, Paten B, Akeson M, Burton AS, Castro-Wallace SL. Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station Using Nanopore Sequencing. Genes (Basel) 2021; 12:genes12010106. [PMID: 33467183 PMCID: PMC7830261 DOI: 10.3390/genes12010106] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
For the past two decades, microbial monitoring of the International Space Station (ISS) has relied on culture-dependent methods that require return to Earth for analysis. This has a number of limitations, with the most significant being bias towards the detection of culturable organisms and the inherent delay between sample collection and ground-based analysis. In recent years, portable and easy-to-use molecular-based tools, such as Oxford Nanopore Technologies’ MinION™ sequencer and miniPCR bio’s miniPCR™ thermal cycler, have been validated onboard the ISS. Here, we report on the development, validation, and implementation of a swab-to-sequencer method that provides a culture-independent solution to real-time microbial profiling onboard the ISS. Method development focused on analysis of swabs collected in a low-biomass environment with limited facility resources and stringent controls on allowed processes and reagents. ISS-optimized procedures included enzymatic DNA extraction from a swab tip, bead-based purifications, altered buffers, and the use of miniPCR and the MinION. Validation was conducted through extensive ground-based assessments comparing current standard culture-dependent and newly developed culture-independent methods. Similar microbial distributions were observed between the two methods; however, as expected, the culture-independent data revealed microbial profiles with greater diversity. Protocol optimization and verification was established during NASA Extreme Environment Mission Operations (NEEMO) analog missions 21 and 22, respectively. Unique microbial profiles obtained from analog testing validated the swab-to-sequencer method in an extreme environment. Finally, four independent swab-to-sequencer experiments were conducted onboard the ISS by two crewmembers. Microorganisms identified from ISS swabs were consistent with historical culture-based data, and primarily consisted of commonly observed human-associated microbes. This simplified method has been streamlined for high ease-of-use for a non-trained crew to complete in an extreme environment, thereby enabling environmental and human health diagnostics in real-time as future missions take us beyond low-Earth orbit.
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Affiliation(s)
| | - Miten Jain
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Hang N. Nguyen
- JES Tech, Houston, TX 77058, USA; (S.S.-R.); (H.N.N.); (C.L.C.)
| | - Richard R. Arnold
- Astronaut Office, NASA Johnson Space Center, Houston, TX 77058, USA; (R.R.A.); (S.M.A.-C.)
| | | | | | | | - Kristen K. John
- Project Management and Systems Engineering Division, NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Sissel Juul
- Oxford Nanopore Technologies, New York, NY 10013, USA;
| | - Daniel J. Turner
- Oxford Nanopore Technologies, Oxford Science Park, Oxford OX4 4DQ, UK; (D.J.T.); (D.S.)
| | - David Stoddart
- Oxford Nanopore Technologies, Oxford Science Park, Oxford OX4 4DQ, UK; (D.J.T.); (D.S.)
| | - Benedict Paten
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Mark Akeson
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Sarah L. Castro-Wallace
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX 77058, USA
- Correspondence: ; Tel.: +1-281-483-7254
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10
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Trojani MC, Lamy B, Ruimy R, Amoretti N, Risso K, Roux C. An unusual Staphylococcus saccharolyticus spondylodiscitis post kyphoplasty: a case report. BMC Infect Dis 2020; 20:539. [PMID: 32703263 PMCID: PMC7379344 DOI: 10.1186/s12879-020-05263-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/16/2020] [Indexed: 11/22/2022] Open
Abstract
Background Staphylococcus saccharolyticus is a rarely encountered coagulase-negative, which grows slowly and its strictly anaerobic staphylococcus from the skin. It is usually considered a contaminant, but some rare reports have described deep-seated infections. Virulence factors remain poorly known, although, genomic analysis highlights pathogenic potential. Case presentation We report a case of Staphylococcus saccharolyticus spondylodiscitis that followed kyphoplasty, a procedure associated with a low rate but possible severe infectious complication (0.46%), and have reviewed the literature. This case specifically stresses the risk of healthcare-associated S. saccharolyticus infection in high-risk patients (those with a history of alcoholism and heavy smoking). Conclusion S. saccharolyticus infection is difficult to diagnose due to microbiological characteristics of this bacterium; it requires timely treatment, and improved infection control procedure should be encouraged for high-risk patients.
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Affiliation(s)
| | - Brigitte Lamy
- Laboratoire de Bactériologie, Hôpital L'archet 2, CHU de Nice, Nice, France.,INSERM U1065, Centre Méditerranéen de Médecine Moléculaire, Equipe 6, Nice, France.,Faculté de Médecine, Université Côte d'Azur, Nice, France
| | - Raymond Ruimy
- Laboratoire de Bactériologie, Hôpital L'archet 2, CHU de Nice, Nice, France.,INSERM U1065, Centre Méditerranéen de Médecine Moléculaire, Equipe 6, Nice, France.,Faculté de Médecine, Université Côte d'Azur, Nice, France
| | - Nicolas Amoretti
- Département de Radiologie, Université Cote d'Azur, CHU de Nice, Nice, France
| | - Karine Risso
- Service d'infectiologie, Université Nice Côte d'Azur, CHU de Nice, Nice, France
| | - Christian Roux
- Département de Rhumatologie, Université Cote d'Azur, LAHMESS EA6309, CNRS, iBV UMR 7277, CHU de Nice, Nice, France
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Staphylococcus saccharolyticus: An Overlooked Human Skin Colonizer. Microorganisms 2020; 8:microorganisms8081105. [PMID: 32718033 PMCID: PMC7465461 DOI: 10.3390/microorganisms8081105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 01/04/2023] Open
Abstract
Coagulase-negative staphylococcal species constitute an important part of the human skin microbiota. In particular, facultative anaerobic species such as Staphylococcus epidermidis and Staphylococcus capitis can be found on the skin of virtually every human being. Here, we applied a culture-independent amplicon sequencing approach to identify staphylococcal species on the skin of healthy human individuals. While S. epidermidis and S. capitis were found as primary residents of back skin, surprisingly, the third most abundant member was Staphylococcus saccharolyticus, a relatively unstudied species. A search of skin metagenomic datasets detected sequences identical to the genome of S. saccharolyticus in diverse skin sites, including the back, forehead, and elbow pit. Although described as a slow-growing anaerobic species, a re-evaluation of its growth behavior showed that S. saccharolyticus can grow under oxic conditions, and, in particular, in a CO2-rich atmosphere. We argue here that S. saccharolyticus was largely overlooked in previous culture-dependent and -independent studies, due to its requirement for fastidious growth conditions and the lack of reference genome sequences, respectively. Future studies are needed to unravel the microbiology and host-interacting properties of S. saccharolyticus and its role as a prevalent skin colonizer.
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Monedeiro F, Pomastowski P, Milanowski M, Ligor T, Buszewski B. Monitoring of Bactericidal Effects of Silver Nanoparticles Based on Protein Signatures and VOC Emissions from Escherichia coli and Selected Salivary Bacteria. J Clin Med 2019; 8:E2024. [PMID: 31752439 PMCID: PMC6912796 DOI: 10.3390/jcm8112024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/19/2019] [Indexed: 01/13/2023] Open
Abstract
Escherichia coli and salivary Klebsiella oxytoca and Staphylococcus saccharolyticus were subjected to different concentrations of silver nanoparticles (AgNPs), namely: 12.5, 50, and 100 µg mL-1. Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) spectra were acquired after specified periods: 0, 1, 4, and 12 h. For study of volatile metabolites, headspace solid-phase microextraction coupled to gas chromatography/mass spectrometry (HS-SPME-GC-MS) was employed-AgNPs were added to bacteria cultures and the headspace was analyzed immediately and after 12 h of incubation. Principal components analysis provided discrimination between clusters of protein profiles belonging to different strains. Canonical correlation, network analysis, and multiple linear regression approach revealed that dimethyl disulfide, dimethyl trisulfide, 2-heptanone, and dodecanal (related to the metabolism of sulfur-containing amino acids and fatty acids synthesis) are exemplary molecular indicators, whose response variation deeply correlated to the interaction with bacteria. Therefore, such species can serve as biomarkers of the agent's effectiveness. The present investigation pointed out that the used approaches can be useful in the monitoring of response to therapeutic treatment based on AgNPs. Furthermore, biochemical mechanisms enrolled in the bactericidal action of nanoparticles can be applied in the development of new agents with enhanced properties.
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Affiliation(s)
- Fernanda Monedeiro
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
- Department of Chemistry, Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-901, Brazil
| | - Paweł Pomastowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Maciej Milanowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Tomasz Ligor
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
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