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Sabat AJ, Durfee T, Baldwin S, Akkerboom V, Voss A, Friedrich AW, Bathoorn E. The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing. Front Cell Infect Microbiol 2024; 14:1368923. [PMID: 38694516 PMCID: PMC11062135 DOI: 10.3389/fcimb.2024.1368923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/25/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Diagnosing Mycoplasma faucium poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements. Methods This study analyzes the complete genome sequence of M. faucium, obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing. Results Genome analysis revealed limited therapeutic options for the M. faucium infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5'-terminally truncated hsdS pseudogenes with overlapping repeats, indicating the potential for forming alternative hsdS variants through recombination. Conclusion This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics.
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Affiliation(s)
- Artur J. Sabat
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tim Durfee
- DNASTAR, Inc., Madison, WI, United States
| | | | - Viktoria Akkerboom
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Andreas Voss
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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Sabat AJ, Wouthuyzen-Bakker M, Rondags A, Hughes L, Akkerboom V, Koutsopetra O, Friedrich AW, Bathoorn E. Case Report: Necrotizing fasciitis caused by Staphylococcus aureus positive for a new sequence variant of exfoliative toxin E. Front Genet 2022; 13:964358. [PMID: 36186447 PMCID: PMC9520408 DOI: 10.3389/fgene.2022.964358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Objectives: Necrotizing fasciitis (NF) caused by S. aureus is a rare, aggressive and rapidly progressing superficial fascia infection with a high mortality rate. The aim of this study was to identify virulence-related genes from a complete genome sequence of a methicillin-susceptible S. aureus (MSSA) isolate recovered from a monomicrobial case of NF. Materials and methods: The MSSA isolate UMCG579 was cultured from a pus collection from the subcutis of a patient with NF. The genome of isolate UMCG579 was sequenced using MinION (Oxford Nanopore) and MiSeq (illumina) platforms. Results: The genome of the UMCG579 isolate was composed of a 2,741,379 bp chromosome and did not harbor any plasmids. Virulence factor profiling identified multiple pore-forming toxin genes in the UMCG579 chromosome, including the Panton-Valentine leukocidin (PVL) genes, and none of the superantigen genes. The UMCG579 isolate harbored a new sequence variant of the recently described ete gene encoding exfoliative toxin (type E). A search in the GenBank database revealed that the new sequence variant (ete2) was exclusively found among isolates (n = 115) belonging to MLST CC152. While the majority of S. aureus ete-positive isolates were recovered from animal sources, S. aureus ete2-positive isolates originated from human carriers and human infections. Comparative genome analysis revealed that the ete2 gene was located on a 8777 bp genomic island. Conclusion: The combination of two heterogeneously distributed potent toxins, ETE2 and PVL, is likely to enhance the pathogenic ability of S. aureus isolates. Since anti-virulence therapies for the treatment of S. aureus infections continue to be explored, the understanding of specific pathogenetic mechanisms may have an important prophylactic and therapeutic value. Nevertheless, the exact contribution of ETE sequence variants to S. aureus virulence in NF infections must be determined.
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Affiliation(s)
- Artur J. Sabat
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- *Correspondence: Artur J. Sabat,
| | - Marjan Wouthuyzen-Bakker
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Angelique Rondags
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Laura Hughes
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Olga Koutsopetra
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alexander W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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Ronco T, Kappel LH, Aragao MF, Biagi N, Svenningsen S, Christensen JB, Permin A, Saaby L, Holmstrøm K, Klitgaard JK, Sabat AJ, Akkerboom V, Monaco M, Tinelli M, Friedrich AW, Jana B, Olsen RH. Insight Into the Anti-staphylococcal Activity of JBC 1847 at Sub-Inhibitory Concentration. Front Microbiol 2022; 12:786173. [PMID: 35069485 PMCID: PMC8766816 DOI: 10.3389/fmicb.2021.786173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistant pathogens constitute a serious global issue and, therefore, novel antimicrobials with new modes of action are urgently needed. Here, we investigated the effect of a phenothiazine derivative (JBC 1847) with high antimicrobial activity on Staphylococcus aureus, using a wide range of in vitro assays, flow cytometry, and RNA transcriptomics. The flow cytometry results showed that JBC 1847 rapidly caused depolarization of the cell membrane, while the macromolecule synthesis inhibition assay showed that the synthesis rates of DNA, RNA, cell wall, and proteins, respectively, were strongly decreased. Transcriptome analysis of S. aureus exposed to sub-inhibitory concentrations of JBC 1847 identified a total of 78 downregulated genes, whereas not a single gene was found to be significantly upregulated. Most importantly, there was downregulation of genes involved in adenosintrifosfat (ATP)-dependent pathways, including histidine biosynthesis, which is likely to correlate with the observed lower level of intracellular ATP in JBC 1847-treated cells. Furthermore, we showed that JBC 1847 is bactericidal against both exponentially growing cells and cells in a stationary growth phase. In conclusion, our results showed that the antimicrobial properties of JBC 1847 were primarily caused by depolarization of the cell membrane resulting in dissipation of the proton motive force (PMF), whereby many essential bacterial processes are affected. JBC 1847 resulted in lowered intracellular levels of ATP followed by decreased macromolecule synthesis rate and downregulation of genes essential for the amino acid metabolism in S. aureus. Bacterial compensatory mechanisms for this proposed multi-target activity of JBC 1847 seem to be limited based on the observed very low frequency of resistance toward the compound.
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Affiliation(s)
- Troels Ronco
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line H. Kappel
- Research Unit of Molecular Microbiology, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Maria F. Aragao
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niccolo Biagi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Svenningsen
- Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jørn B. Christensen
- Department of Chemistry, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Janne K. Klitgaard
- Research Unit of Molecular Microbiology, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Research Unit of Clinical Microbiology, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Artur J. Sabat
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Monica Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Tinelli
- Division of Infectious and Tropical Diseases, Hospital of Lodi, Lodi, Italy
| | - Alexander W. Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bimal Jana
- Department of Biology, Boston College, Chestnut Hill, MA, United States
| | - Rikke H. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Sabat AJ, Pantano D, Akkerboom V, Bathoorn E, Friedrich AW. Pseudomonas aeruginosa and Staphylococcus aureus virulence factors as biomarkers of infection. Biol Chem 2021; 402:1565-1573. [PMID: 34505460 DOI: 10.1515/hsz-2021-0243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022]
Abstract
The gold standard for the diagnosis of bacterial infections in clinical samples is based on culture tests that are time-consuming and labor-intense. For these reasons, an extraordinary effort has been made to identify biomarkers as the tools for sensitive, rapid and accurate identification of pathogenic microorganisms. Moreover, biomarkers have been tested to distinguish colonization from infection, monitor disease progression, determine the clinical status of patients or predict clinical outcomes. This mini-review describes Pseudomonas aeruginosa and Staphylococcus aureus biomarkers, which contribute to pathogenesis and have been used in culture-independent bacterial identification directly from patient samples.
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Affiliation(s)
- Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, NL-9713 GZ Groningen, The Netherlands
| | - Daniele Pantano
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, NL-9713 GZ Groningen, The Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, NL-9713 GZ Groningen, The Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, NL-9713 GZ Groningen, The Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, NL-9713 GZ Groningen, The Netherlands
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5
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Sabat AJ, Bathoorn E, Chlebowicz-Fliss MA, Akkerboom V, Kamphuis I, Dos Santos CO, Friedrich AW. Misidentification of meticillin-resistant Staphylococcus aureus by the Cepheid Xpert MRSA NxG assay, the Netherlands, February to March 2021. ACTA ACUST UNITED AC 2021; 26. [PMID: 34533121 PMCID: PMC8447827 DOI: 10.2807/1560-7917.es.2021.26.37.2100800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe two false-negative results in the detection of meticillin-resistant Staphylococcus aureus (MRSA) of sequence type 398 and spa type t011 using the Cepheid Xpert MRSA NxG assay. The isolates were recovered in late February and early March 2021 from two patients in different hospitals in the northern Netherlands. Variations between the two isolate genomes indicate that this MRSA strain might have been spreading for some time and could have disseminated to other regions of the Netherlands and other European countries.
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Affiliation(s)
- Artur J Sabat
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Erik Bathoorn
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Monika A Chlebowicz-Fliss
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Viktoria Akkerboom
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Inge Kamphuis
- Isala Hospital, Laboratory for Medical Microbiology and Infectious Diseases, Zwolle, the Netherlands
| | | | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
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6
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Sabat AJ, Bathoorn E, Becker K, Akkerboom V, Miskoski M, Durfee T, Friedrich AW. Staphylococcal cassette chromosome mec containing a novel mec gene complex, B4. J Antimicrob Chemother 2021; 76:1986-1990. [PMID: 33993306 PMCID: PMC8283725 DOI: 10.1093/jac/dkab154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Objectives To describe a new subclass of mec class B complex identified in Staphylococcus epidermidis. Methods Four S. epidermidis isolates obtained from bloodstream infections in patients at University Medical Center Groningen (UMCG) were analysed by phenotypic antibiotic susceptibility testing and WGS. Results Sequence analysis revealed a new staphylococcal cassette chromosome mec (SCCmec) structure in isolate UMCG335. In this structure, plasmid pUB110 was found to be integrated into SCCmec IVc, creating a new SCCmec subtype, IVUMCG335. SCCmec IVc and a copy of plasmid pUB110 were found in other isolates, UMCG364 and UMCG341, respectively, indicating a probability that SCCmec IVUMCG335 could have evolved at the UMCG. SCCmec of UMCG337 contained a new genetic organization of the mec complex (IS431-ΔmecR1-mecA-IS431-pUB110-IS431-ψIS1272) that we have named B4. This new subclass of mec class B complex originated by IS431-mediated inversion of the DNA segment encompassing the plasmid and most of the genes of the mec complex with the exception of IS1272. As the SCCmec organization in UMCG337 differed by the inversion of an ∼10 kb sequence compared with SCCmec IVUMCG335, we have named it SCCmec subtype IVUMCG337. Isolates UMCG335 and UMCG337 carrying SCCmec IVUMCG335 and IVUMCG337, respectively, were associated with a restriction-modification system and a CRISPR-Cas system, creating a composite island of almost 70 kb. Conclusions Our findings highlight the importance of IS431 in the evolution of the SCCmec region. The increasing genetic diversity identified in the SCCmec elements imposes a great challenge for SCCmec typing methods and highlights possible difficulties with the SCCmec nomenclature.
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Affiliation(s)
- Artur J Sabat
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Erik Bathoorn
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Viktoria Akkerboom
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | | | | | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
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7
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Deplano A, Dodémont M, Denis O, Westh H, Gumpert H, Larsen AR, Larsen J, Kearns A, Pichon B, Layer F, Schulte B, Wolz C, Spiliopoulou I, Brennan G, Empel J, Hryniewicz W, de Lencastre H, Faria NA, Codita I, Sabat AJ, Friedrich AW, Deurenberg RH, Tristan A, Laurent F, Vandenesch F. European external quality assessments for identification, molecular typing and characterization of Staphylococcus aureus. J Antimicrob Chemother 2019; 73:2662-2666. [PMID: 30099486 DOI: 10.1093/jac/dky260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/07/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives We present the results of two European external quality assessments (EQAs) conducted in 2014 and 2016 under the auspices of the Study Group on Staphylococci and Staphylococcal Infections of ESCMID. The objective was to assess the performance of participating centres in characterizing Staphylococcus aureus using their standard in-house phenotypic and genotypic protocols. Methods A total of 11 well-characterized blindly coded S. aureus (n = 9), Staphylococcus argenteus (n = 1) and Staphylococcus capitis (n = 1) strains were distributed to participants for analysis. Species identification, MIC determination, antimicrobial susceptibility testing, antimicrobial resistance and toxin gene detection and molecular typing including spa typing, SCCmec typing and MLST were performed. Results Thirteen laboratories from 12 European countries participated in one EQA or both EQAs. Despite considerable diversity in the methods employed, good concordance (90%-100%) with expected results was obtained. Discrepancies were observed for: (i) identification of the S. argenteus strain; (ii) phenotypic detection of low-level resistance to oxacillin in the mecC-positive strain; (iii) phenotypic detection of the inducible MLSB strain; and (iv) WGS-based detection of some resistance and toxin genes. Conclusions Overall, good concordance (90%-100%) with expected results was observed. In some instances, the accurate detection of resistance and toxin genes from WGS data proved problematic, highlighting the need for validated and internationally agreed-on bioinformatics pipelines before such techniques are implemented routinely by microbiology laboratories. We strongly recommend all national reference laboratories and laboratories acting as referral centres to participate in such EQA initiatives.
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Affiliation(s)
- Ariane Deplano
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Magali Dodémont
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Olivier Denis
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Henrik Westh
- MRSA Knowledge Center, Hvidovre Hospital, Kettegard Alle 30, Hvidrove, Denmark.,Institute of Clinical Medicine, Faculty of Medicine and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heidi Gumpert
- MRSA Knowledge Center, Hvidovre Hospital, Kettegard Alle 30, Hvidrove, Denmark
| | - Anders Rhod Larsen
- National Reference Laboratory for Antimicrobial Resistance and Staphylococci, Statens Serum Institut, Artllerivej 5, Copenhagen, Denmark
| | - Jesper Larsen
- National Reference Laboratory for Antimicrobial Resistance and Staphylococci, Statens Serum Institut, Artllerivej 5, Copenhagen, Denmark
| | - Angela Kearns
- Staphylococcus Reference Service, National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Bruno Pichon
- Staphylococcus Reference Service, National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Franziska Layer
- Nationale referenzzeebtrum fûr Staphylokokken, Robert Koch Institute, Burgstraße 37, Wernigerode, Germany
| | - Berit Schulte
- Institute für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, Germany
| | - Christiane Wolz
- Institute für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, Germany
| | - Iris Spiliopoulou
- National Staphylococcal Reference Laboratory, Department of Microbiology, School of Medicine, University of Patras, Rion, Patras, Greece
| | - Gráinne Brennan
- National MRSA Reference Laboratory, St James's Hospital, James's Street, Dublin, Ireland
| | - Joanna Empel
- Department of Epidemiology and Clinical Microbiology, Narodowy Instytut Leków, Chelmska 30/34, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, Narodowy Instytut Leków, Chelmska 30/34, Warsaw, Poland
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.,Laboratory of Microbiology & Infectious Diseases, The Rockefeller University, 1230 York Ave., New York, NY, USA
| | - Nuno Alexandre Faria
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.,Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Irina Codita
- Cantazuno National Institute of Research, Staphylococcus Reference Laboratory, INC Cantacuzino Splaiul Independentei 103, Bucarest, Romania
| | - Artur J Sabat
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Ruud H Deurenberg
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Anne Tristan
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
| | - Frédéric Laurent
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
| | - François Vandenesch
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
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Kosecka-Strojek M, Sabat AJ, Akkerboom V, Becker K, van Zanten E, Wisselink G, Miedzobrodzki J, Kooistra-Smid AMDM, Friedrich AW. Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region. Front Cell Infect Microbiol 2019; 9:278. [PMID: 31456949 PMCID: PMC6698797 DOI: 10.3389/fcimb.2019.00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
Many members of the Staphylococcus genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy. The aim of this study was to develop a careful assignment scheme for staphylococcal species based on next-generation sequencing (NGS) of the 16S-23S rRNA region. All reference staphylococcal strains were identified at the species level using Sanger sequencing of the 16S rRNA, sodA, tuf, and rpoB genes and NGS of the 16S-23S rRNA region. To broaden the database, an additional 100 staphylococcal strains, including 29 species, were identified by routine diagnostic methods, 16S rRNA Sanger sequencing and NGS of the 16S-23S rRNA region. The results enabled development of reference sequences encompassing the 16S-23S rRNA region for 50 species (including one newly proposed species) and 6 subspecies of the Staphylococcus genus. This study showed sodA and rpoB targets were the most discriminative but NGS of the 16S-23S rRNA region was more discriminative than tuf gene sequencing and much more discriminative than 16S rRNA gene sequencing. Almost all Staphylococcus species could be distinguished when the max score was 99.0% or higher and the sequence similarity between the best and second best species was equal to or >0.2% (min. 9 nucleotides). This study allowed development of reference sequences for 21 staphylococcal species and enrichment for 29 species for which sequences were publicly available. We confirmed the usefulness of NGS of the 16S-23S rRNA region by identifying the whole species content in 45 clinical samples and comparing the results to those obtained using routine diagnostic methods. Based on the developed reference database, all staphylococcal species can be reliably detected based on the 16S-23S rRNA sequences in samples composed of both single species and more complex polymicrobial communities. This study will be useful for introduction of a novel diagnostic tool, which undoubtedly is an improvement for reliable species identification in polymicrobial samples. The introduction of this new method is hindered by a lack of reference sequences for the 16S-23S rRNA region for many bacterial species. The results will allow identification of all Staphylococcus species, which are clinically relevant pathogens.
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Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Evert van Zanten
- Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Guido Wisselink
- Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna M D Mirjam Kooistra-Smid
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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9
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Sabat AJ, Tinelli M, Grundmann H, Akkerboom V, Monaco M, Del Grosso M, Errico G, Pantosti A, Friedrich AW. Daptomycin Resistant Staphylococcus aureus Clinical Strain With Novel Non-synonymous Mutations in the mprF and vraS Genes: A New Insight Into Daptomycin Resistance. Front Microbiol 2018; 9:2705. [PMID: 30459746 PMCID: PMC6232378 DOI: 10.3389/fmicb.2018.02705] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/23/2018] [Indexed: 11/25/2022] Open
Abstract
Objectives: Daptomycin (DAP) resistance in Staphylococcus aureus is uncommon but there are increasing reports of the emergence of resistance during DAP therapy. Most clinical DAP-resistant S. aureus isolates investigated carried mutations in the mprF gene. The aim of this study was to identify mutations between a clinical pair of methicillin-susceptible S. aureus (MSSA) isolates (DAP-susceptible and DAP-resistant). Additionally, the activity of genes previously associated with DAP resistance was assessed. Materials and Methods: Two MSSA isolates from patient with left-sided endocarditis were analyzed by whole genome sequencing (WGS) and reverse transcription-quantitative real-time PCR (RT-qPCR). The first isolate, DAP-susceptible, was obtained before initiation of treatment and the second isolate, DAP-resistant, was recovered after 4 weeks of DAP therapy. Results: Comparison of complete genomes of DAP-susceptible and its DAP-resistant variant identified two non-synonymous and one synonymous mutations. The non-synonymous mutations consisted of a S829L substitution in mprF and a T331I substitution in vraS. The RT-qPCR experiments revealed an increased expression of vraS, dltA, mprF, and sceD genes in DAP-resistant variant. Strikingly, the expression of dltA and mprF genes was significantly downregulated by DAP. Conclusion: The mprF and vraS genes were previously associated with DAP resistance, however, none of the mutations described in this study had been previously identified and linked to DAP resistance. Moreover, we provide a new insight into the DAP action on S. aureus, in which the expression of key genes in DAP resistance is decreased by the antibiotic.
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Affiliation(s)
- Artur J Sabat
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Marco Tinelli
- Division of Infectious and Tropical Diseases, Hospital of Lodi, Lodi, Italy
| | - Hajo Grundmann
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Monica Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Del Grosso
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Giulia Errico
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Alexander W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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10
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Bonar EA, Bukowski M, Hydzik M, Jankowska U, Kedracka-Krok S, Groborz M, Dubin G, Akkerboom V, Miedzobrodzki J, Sabat AJ, Friedrich AW, Wladyka B. Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Staphylococcus aureus Strains. Front Cell Infect Microbiol 2018; 8:313. [PMID: 30237986 PMCID: PMC6136393 DOI: 10.3389/fcimb.2018.00313] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen of humans and warm-blooded animals and presents a growing threat in terms of multi-drug resistance. Despite numerous studies, the basis of staphylococcal virulence and switching between commensal and pathogenic phenotypes is not fully understood. Using genomics, we show here that S. aureus strains exhibiting virulent (VIR) and non-virulent (NVIR) phenotypes in a chicken embryo infection model genetically fall into two separate groups, with the VIR group being much more cohesive than the NVIR group. Significantly, the genes encoding known staphylococcal virulence factors, such as clumping factors, are either found in different allelic variants in the genomes of NVIR strains (compared to VIR strains) or are inactive pseudogenes. Moreover, the pyruvate carboxylase and gamma-aminobutyrate permease genes, which were previously linked with virulence, are pseudogenized in NVIR strain ch22. Further, we use comprehensive proteomics tools to characterize strains that show opposing phenotypes in a chicken embryo virulence model. VIR strain CH21 had an elevated level of diapolycopene oxygenase involved in staphyloxanthin production (protection against free radicals) and expressed a higher level of immunoglobulin-binding protein Sbi on its surface compared to NVIR strain ch22. Furthermore, joint genomic and proteomic approaches linked the elevated production of superoxide dismutase and DNA-binding protein by NVIR strain ch22 with gene duplications.
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Affiliation(s)
- Emilia A Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marcin Hydzik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Magdalena Groborz
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur J Sabat
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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11
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Bonar E, Wojcik I, Jankowska U, Kedracka-Krok S, Bukowski M, Polakowska K, Lis MW, Kosecka-Strojek M, Sabat AJ, Dubin G, Friedrich AW, Miedzobrodzki J, Dubin A, Wladyka B. Identification of Secreted Exoproteome Fingerprints of Highly-Virulent and Non-Virulent Staphylococcus aureus Strains. Front Cell Infect Microbiol 2016; 6:51. [PMID: 27242969 PMCID: PMC4874363 DOI: 10.3389/fcimb.2016.00051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/19/2016] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus is a commensal inhabitant of skin and mucous membranes in nose vestibule but also an important opportunistic pathogen of humans and livestock. The extracellular proteome as a whole constitutes its major virulence determinant; however, the involvement of particular proteins is still relatively poorly understood. In this study, we compared the extracellular proteomes of poultry-derived S. aureus strains exhibiting a virulent (VIR) and non-virulent (NVIR) phenotype in a chicken embryo experimental infection model with the aim to identify proteomic signatures associated with the particular phenotypes. Despite significant heterogeneity within the analyzed proteomes, we identified alpha-haemolysin and bifunctional autolysin as indicators of virulence, whereas glutamylendopeptidase production was characteristic for non-virulent strains. Staphopain C (StpC) was identified in both the VIR and NVIR proteomes and the latter fact contradicted previous findings suggesting its involvement in virulence. By supplementing NVIR, StpC-negative strains with StpC, and comparing the virulence of parental and supplemented strains, we demonstrated that staphopain C alone does not affect staphylococcal virulence in a chicken embryo model.
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Affiliation(s)
- Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Iwona Wojcik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University Krakow, Poland
| | - Sylwia Kedracka-Krok
- Malopolska Centre of Biotechnology, Jagiellonian UniversityKrakow, Poland; Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Klaudia Polakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Marcin W Lis
- Department of Veterinary and Animal Reproduction and Welfare, Faculty of Animal Welfare, University of Agriculture in Krakow Krakow, Poland
| | - Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian UniversityKrakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Adam Dubin
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
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12
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Ilczyszyn WM, Sabat AJ, Akkerboom V, Szkarlat A, Klepacka J, Sowa-Sierant I, Wasik B, Kosecka-Strojek M, Buda A, Miedzobrodzki J, Friedrich AW. Clonal Structure and Characterization of Staphylococcus aureus Strains from Invasive Infections in Paediatric Patients from South Poland: Association between Age, spa Types, Clonal Complexes, and Genetic Markers. PLoS One 2016; 11:e0151937. [PMID: 26992009 PMCID: PMC4798296 DOI: 10.1371/journal.pone.0151937] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/07/2016] [Indexed: 12/20/2022] Open
Abstract
The aim of current study was to examine clonal structure and genetic profile of invasive Staphylococcus aureus isolates recovered from infants and children treated at the Jagiellonian University Children’s Hospital of Krakow, Poland. The 107 invasive S. aureus isolates, collected between February 2012 and August 2014, were analysed retrospectively. Antimicrobial susceptibility testing, spa typing and DNA microarray analysis were performed to determine clonal distribution, diversity and gene content in regard to patients characteristics. In total, 107 isolates were recovered from 88 patients with clinical symptoms of invasive bacterial infection. The final set of 92 non-duplicate samples included 38 MRSA isolates. Additionally, a set of 54 S. aureus isolates collected during epidemiological screening was genotyped and analysed. There were 72 healthcare-associated (HCA) and 20 community-onset (CO) infection events caused by 33 and 5 MRSA isolates, respectively. The majority of isolates were affiliated with the major European clonal complexes CC5 (t003, spa-CC 002), CC45 (spa-CC 015), CC7 or CC15 (t084, t091, spa-CC 084). Two epidemic clones (CC5-MRSA-II or CC45-MRSA-IV) dominated among MRSA isolates, while MSSA population contained 15 different CCs. The epidemiological screening isolates belonged to similar genetic lineages as those collected from invasive infection cases. The HCA infection events, spa types t003, t2642 or CC5 were significantly associated with infections occurring in neonates and children under 5 years of age. Moreover, carriage of several genetic markers, including erm(A), sea (N315), egc-cluster, chp was significantly higher in isolates obtained from children in this age group. The spa types t091 and t008 were underrepresented among patients aged 5 years or younger, whereas spa type t008, CC8 and presence of splE was associated with infection in children aged 10 years or older. The HCA-MRSA strains were most frequently found in children under 5 years, although the majority of invasive infections was associated with MSSA strains. Moreover, an association between age group of children from the study population and a specific strain genotype (spa type, clonal complex or genetic content) was observed among the patients.
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Affiliation(s)
- Weronika M Ilczyszyn
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anna Szkarlat
- Department of Clinical Microbiology, Children's University Hospital, Jagiellonian University, Krakow, Poland
| | - Joanna Klepacka
- Department of Clinical Microbiology, Children's University Hospital, Jagiellonian University, Krakow, Poland
| | - Iwona Sowa-Sierant
- Department of Clinical Microbiology, Children's University Hospital, Jagiellonian University, Krakow, Poland
| | - Barbara Wasik
- Department of Clinical Microbiology, Children's University Hospital, Jagiellonian University, Krakow, Poland
| | - Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aneta Buda
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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13
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Pournaras S, Sabat AJ, Grundmann H, Hendrix R, Tsakris A, Friedrich AW. Driving Forces of Mechanisms Regulating Oxacillin-Resistance Phenotypes of MRSA: Truly Oxacillin-Susceptible mecA-Positive Staphylococcus aureus Clinical Isolates also Exist. Curr Pharm Des 2016; 21:2048-53. [PMID: 25760336 DOI: 10.2174/1381612821666150310103754] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/05/2015] [Indexed: 11/22/2022]
Abstract
As MRSA are considered Staphylococcus aureus isolates with oxacillin minimum inhibitory concentration (MIC) of ≥4 mg/L or harboring the mecA gene. However, the presence of mecA does not necessarily lead to oxacillin resistance and mecA gene-carrying isolates may have oxacillin MIC within the susceptible range (≥2 mg/L). During the last few years it has become apparent that oxacillin-susceptible (OS) mecA-positive S. aureus isolates (commonly called OS-MRSA) are rather commonly detected worldwide and may remain undiagnosed using phenotypic susceptibility testing methods. This review will summarize the current reports on OS-MRSA isolations and the underlying mechanisms regulating the expression of oxacillin resistance and also oxacillin susceptibility in mecA-positive S. aureus isolates. As MRSA commonly cause severe infections against which effective therapies are limited, understanding of these mechanisms could enable the identification of new targets for the treatment or reversion of the MRSA phenotype.
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14
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Wladyka B, Piejko M, Bzowska M, Pieta P, Krzysik M, Mazurek Ł, Guevara-Lora I, Bukowski M, Sabat AJ, Friedrich AW, Bonar E, Międzobrodzki J, Dubin A, Mak P. A peptide factor secreted by Staphylococcus pseudintermedius exhibits properties of both bacteriocins and virulence factors. Sci Rep 2015; 5:14569. [PMID: 26411997 PMCID: PMC4585962 DOI: 10.1038/srep14569] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/01/2015] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus pseudintermedius is a common commensal bacterium colonizing the skin and mucosal surfaces of household animals. However, it has recently emerged as a dangerous opportunistic pathogen, comparable to S. aureus for humans. The epidemiological situation is further complicated by the increasing number of methicillin-resistant S. pseudintermedius infections and evidence of gene transmission driving antibiotic resistance between staphylococci colonizing human and zoonotic hosts. In the present study, we describe a unique peptide, BacSp222, that possesses features characteristic of both bacteriocins and virulence factors. BacSp222 is secreted in high quantities by S. pseudintermedius strain 222 isolated from dog skin lesions. This linear, fifty-amino-acid highly cationic peptide is plasmid-encoded and does not exhibit significant sequence similarities to any other known peptides or proteins. BacSp222 kills gram-positive bacteria (at doses ranging from 0.1 to several micromol/l) but also demonstrates significant cytotoxic activities towards eukaryotic cells at slightly higher concentrations. Moreover, at nanomolar concentrations, the peptide also possesses modulatory properties, efficiently enhancing interferon gamma-induced nitric oxide release in murine macrophage-like cell lines. BacSp222 appears to be one of the first examples of multifunctional peptides that breaks the convention of splitting bacteriocins and virulence factors into two unrelated groups.
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Affiliation(s)
- Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Marcin Piejko
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,3rd Department of General Surgery, Jagiellonian University Medical College, 31-008 Krakow, Poland
| | - Monika Bzowska
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Piotr Pieta
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Monika Krzysik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Łukasz Mazurek
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Ibeth Guevara-Lora
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michał Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jacek Międzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Adam Dubin
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Paweł Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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15
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Amissah NA, Chlebowicz MA, Ablordey A, Sabat AJ, Tetteh CS, Prah I, van der Werf TS, Friedrich AW, van Dijl JM, Rossen JW, Stienstra Y. Molecular Characterization of Staphylococcus aureus Isolates Transmitted between Patients with Buruli Ulcer. PLoS Negl Trop Dis 2015; 9:e0004049. [PMID: 26360794 PMCID: PMC4567303 DOI: 10.1371/journal.pntd.0004049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/11/2015] [Indexed: 12/18/2022] Open
Abstract
Background Buruli ulcer (BU) is a skin infection caused by Mycobacterium ulcerans. The wounds of most BU patients are colonized with different microorganisms, including Staphylococcus aureus. Methodology This study investigated possible patient-to-patient transmission events of S. aureus during wound care in a health care center. S. aureus isolates from different BU patients with overlapping visits to the clinic were whole-genome sequenced and analyzed by a gene-by-gene approach using SeqSphere+ software. In addition, sequence data were screened for the presence of genes that conferred antibiotic resistance. Principal Findings SeqSphere+ analysis of whole-genome sequence data confirmed transmission of methicillin resistant S. aureus (MRSA) and methicillin susceptible S. aureus among patients that took place during wound care. Interestingly, our sequence data show that the investigated MRSA isolates carry a novel allele of the fexB gene conferring chloramphenicol resistance, which had thus far not been observed in S. aureus. Buruli ulcer (BU) is a skin infection caused by Mycobacterium ulcerans. The wounds of most BU patients are colonized with different microorganisms, including Staphylococcus aureus. This study investigated patient-to-patient transmission events during wound care in a health care center. S. aureus isolates from patients who visited the health center at the same time points were analyzed using whole-genome sequencing. Analysis of sequence data confirmed transmission of methicillin resistant S. aureus and methicillin susceptible S. aureus among patients that took place during wound care.
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Affiliation(s)
- Nana Ama Amissah
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- * E-mail:
| | - Monika A. Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Artur J. Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Caitlin S. Tetteh
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Isaac Prah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Tjip S. van der Werf
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alex W. Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - John W. Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ymkje Stienstra
- Department of Internal Medicine/Infectious Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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16
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Sabat AJ, Pournaras S, Akkerboom V, Tsakris A, Grundmann H, Friedrich AW. Whole-genome analysis of an oxacillin-susceptible CC80 mecA-positive Staphylococcus aureus clinical isolate: insights into the mechanisms of cryptic methicillin resistance. J Antimicrob Chemother 2015. [PMID: 26198147 DOI: 10.1093/jac/dkv210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The mec and bla systems, among other genetic factors, are critical in regulating the expression of methicillin resistance in Staphylococcus aureus. We examined by WGS a naturally occurring oxacillin-susceptible mecA-positive S. aureus isolate to identify the mechanism conferring oxacillin susceptibility. METHODS The mecA-positive oxacillin-susceptible S. aureus isolate GR2 (penicillin and oxacillin MICs 0.094 and 1 mg/L, respectively), belonging to clonal complex 80, was characterized. DNA fragment libraries were sequenced on Roche 454 and Illumina MiSeq sequencers and de novo assembly of the genome was generated using SeqMan NGen software. Plasmid curing was conducted by SDS treatment. Expression of mecA was quantified without/with β-lactam pressure. RESULTS The genome of GR2 consisted of a 2 792 802 bp chromosome and plasmids pGR2A (28 895 bp) and pGR2B (2473 bp). GR2 carried SCCmec type IV, with a truncated/non-functional mecR1 gene and no mecI. A single copy of the bla system, with an organization unique for S. aureus, was found, harboured by plasmid pGR2A. Particularly, the blaZ gene was orientated like its regulatory genes, blaI and blaR1, and a gene encoding transposase IS66 was integrated between blaZ and the regulatory genes deleting the 5'-end of blaR1; blaI, encoding blaZ/mecA repressor, was intact. After plasmid loss, GR2 became penicillin and oxacillin resistant (MICs 0.5 and 6 mg/L, respectively). CONCLUSIONS We can conclude that after exposure to β-lactams, the non-functional BlaR1 does not cleave the mecA repressor BlaI, derepression does not occur and mecA is not efficiently expressed. Removal of the bla system after curing of pGR2A allows constitutive expression of mecA, resulting in oxacillin and penicillin resistance.
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Affiliation(s)
- Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Spyros Pournaras
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Microbiology, Medical School, University of Athens, Athens, Greece
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Athanassios Tsakris
- Department of Microbiology, Medical School, University of Athens, Athens, Greece
| | - Hajo Grundmann
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Sabat AJ, Ilczyszyn WM, van Rijen M, Akkerboom V, Sinha B, Kluytmans J, Miedzobrodzki J, Grundmann H, Friedrich AW. Genome-wide analysis reveals two novel mosaic regions containing an ACME with an identical DNA sequence in the MRSA ST398-t011 and MSSA ST8-t008 isolates. J Antimicrob Chemother 2015; 70:1298-302. [PMID: 25634990 DOI: 10.1093/jac/dku531] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/01/2014] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The presence of the arginine catabolic mobile element (ACME) in Staphylococcus aureus has been reported to enhance the colonization of the human host. The aim of this study was to determine the genetic organization of composite islands harbouring ACME. METHODS Two ACME-positive S. aureus isolates obtained during two different surveys conducted in the Netherlands and Poland were characterized in this study. The isolates were analysed by spa typing, DNA microarrays and whole-genome sequencing. RESULTS The two isolates harboured a truncated yet fully functional ACME type II with an identical nucleotide sequence, but differed in their adjacent mobile genetic elements. The first strain was a livestock-associated ST398-t011 MRSA, which had a staphylococcal cassette chromosome mec (SCCmec) composite island composed of SCCpls adjacent to orfX followed by ACME type II and SCCmec type IVa. The second ACME-positive isolate was an ST8-t008 MSSA. Its composite island showed an SCC-like element carrying the ccrC gene followed by ACME II. CONCLUSIONS This is the first report of an ACME in a livestock-associated MRSA ST398. It is also the first presentation of an ACME composite island structure in an MSSA isolate. Our findings indicate an extensive mosaicism of composite islands in S. aureus, which has implications for the transmissibility among humans and thus for public health.
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Affiliation(s)
- Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Weronika M Ilczyszyn
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Miranda van Rijen
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bhanu Sinha
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Kluytmans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Hajo Grundmann
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Grundmann H, Schouls LM, Aanensen DM, Pluister GN, Tami A, Chlebowicz M, Glasner C, Sabat AJ, Weist K, Heuer O, Friedrich AW. The dynamic changes of dominant clones of Staphylococcus aureus causing bloodstream infections in the European region: results of a second structured survey. ACTA ACUST UNITED AC 2014; 19. [PMID: 25523972 DOI: 10.2807/1560-7917.es2014.19.49.20987] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Staphylococcus aureus is one of the most important human pathogens and meticillin-resistant S. aureus (MRSA) presents a major cause of healthcare- and community-acquired infections. This study investigated the spatial and temporal changes of S. aureus causing bacteraemia in Europe over a five-year interval and explored the possibility of integrating pathogen-based typing data with epidemiological and clinical information at a European level. Between January 2011 and July 2011, 350 laboratories serving 453 hospitals in 25 countries collected 3,753 isolates (meticillin-sensitive S. aureus (MSSA) and MRSA) from patients with S. aureus bloodstream infections. All isolates were sent to the national staphylococcal reference laboratories and characterised by quality-controlled spa typing. Data were uploaded to an interactive web-based mapping tool. A wide geographical distribution of spa types was found, with some prevalent in all European countries. MSSA was more diverse than MRSA. MRSA differed considerably between countries with major international clones expanding or receding when compared to a 2006 survey. We provide evidence that a network approach of decentralised typing and visualisation of aggregated data using an interactive mapping tool can provide important information on the dynamics of S. aureus populations such as early signalling of emerging strains, cross-border spread and importation by travel.
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Affiliation(s)
- H Grundmann
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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19
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Aiken AM, Mutuku IM, Sabat AJ, Akkerboom V, Mwangi J, Scott JAG, Morpeth SC, Friedrich AW, Grundmann H. Carriage of Staphylococcus aureus in Thika Level 5 Hospital, Kenya: a cross-sectional study. Antimicrob Resist Infect Control 2014; 3:22. [PMID: 25057351 PMCID: PMC4107749 DOI: 10.1186/2047-2994-3-22] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 06/23/2014] [Indexed: 11/17/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen but little is known about its circulation in hospitals in developing countries. We aimed to describe carriage of S.aureus amongst inpatients in a mid-sized Kenyan government hospital. Methods We determined the frequency of S.aureus and MRSA carriage amongst inpatients in Thika Hospital, Kenya by means of repeated cross-sectional ward surveys. For all S.aureus isolates, we performed antibiotic susceptibility tests, genomic profiling using a DNA microarray and spa typing and MLST. Results In this typical mid-sized Kenyan Government hospital, we performed 950 screens for current carriage of S.aureus amongst inpatients over a four month period. We detected S.aureus carriage (either MSSA or MRSA) in 8.9% (85/950; 95%CI 7.1-10.8) of inpatient screens, but patients with multiple screens were more likely have detection of carriage. MRSA carriage was rare amongst S.aureus strains carried by hospital inpatients – only 7.0% (6/86; 95%CI 1.5-12.5%) of all isolates were MRSA. Most MRSA (5/6) were obtained from burns patients with prolonged admissions, who only represented a small proportion of the inpatient population. All MRSA strains were of the same clone (MLST ST239; spa type t037) with concurrent resistance to multiple antibiotic classes. MSSA isolates were diverse and rarely expressed antibiotic resistance except against benzyl-penicillin and co-trimoxazole. Conclusions Although carriage rates for S.aureus and the MRSA prevalence in this Kenyan hospital were both low, burns patient were identified as a high risk group for carriage. The high frequency of genetically indistinguishable isolates suggests that there was local transmission of both MRSA and MSSA.
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Affiliation(s)
- Alexander M Aiken
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK ; Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Irene M Mutuku
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - J Anthony G Scott
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK ; Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Susan C Morpeth
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK ; Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hajo Grundmann
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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van der Kooi-Pol MM, Sadaghian Sadabad M, Duipmans JC, Sabat AJ, Stobernack T, Omansen TF, Westerhout-Pluister GN, Jonkman MF, Harmsen HJM, van Dijl JM. Topography of distinct Staphylococcus aureus types in chronic wounds of patients with epidermolysis bullosa. PLoS One 2013; 8:e67272. [PMID: 23825650 PMCID: PMC3692413 DOI: 10.1371/journal.pone.0067272] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/17/2013] [Indexed: 11/26/2022] Open
Abstract
The opportunistic pathogen Staphylococcus aureus is known to interfere with wound healing and represents a significant risk factor for wound infections and invasive disease. It is generally assumed that one individual is predominantly colonized by one S. aureus type. Nevertheless, patients with the genetic blistering disease epidermolysis bullosa (EB) often carry multiple S. aureus types. We therefore investigated whether different S. aureus types are present in individual wounds of EB patients and, if so, how they are spatially distributed. The staphylococcal topography in chronic wounds was mapped by replica-plating of used bandages and subsequent typing of S. aureus isolates. Individual chronic wounds of five patients contained up to six different S. aureus types. Unexpectedly, distinct S. aureus types formed micro-colonies that were located in close proximity and sometimes even overlapped. While some adjacent S. aureus isolates were closely related, others belonged to distinct molecular complexes. We conclude that the general assumption that one individual is predominantly colonized by one type of S. aureus does not apply to chronic wounds of EB patients. We consider this observation important, not only for EB patients, but also for other patients with chronic wounds in view of the potential risk for severe staphylococcal infections.
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Affiliation(s)
- Magdalena M. van der Kooi-Pol
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Mehdi Sadaghian Sadabad
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - José C. Duipmans
- Department of Dermatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Artur J. Sabat
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Tim Stobernack
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Till F. Omansen
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Gerlinde N. Westerhout-Pluister
- Laboratory for Infectious Diseases and Perinatal Screening, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marcel F. Jonkman
- Department of Dermatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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Chlebowicz MA, Bosch T, Sabat AJ, Arends JP, Grundmann H, van Dijl JM, Buist G. Distinction of Staphylococcal Cassette Chromosome mec type V elements from Staphylococcus aureus ST398. Int J Med Microbiol 2013; 303:422-32. [PMID: 23786828 DOI: 10.1016/j.ijmm.2013.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/05/2013] [Accepted: 05/20/2013] [Indexed: 11/16/2022] Open
Abstract
Methicillin resistant S. aureus (MRSA) is a major threat for human health and well-being. In recent years, it has become clear that livestock is a potential reservoir for MRSA, most livestock-associated isolates belonging to the ST398 lineage. Importantly, ST398 strains were also reported as causative agents of severe invasive infections in humans with no evidence for livestock associations. Here we document the sequence of the J1 region of the type V (5C2&5) SCCmec element and its right chromosomal junction in the clinical PVL-positive ST398 MRSA isolate UMCG-M4. Sequence comparisons show that this SCCmec element and related type V elements from other S. aureus isolates share a common core structure, but differ substantially in the so-called J1 region. Additional PCR analyses and typing studies indicate that the J1 region of strain UMCG-M4 is specific for SCCmec elements of PVL-positive ST398 isolates. Lastly, we show that the sequenced right chromosomal junction is invariant in strains of the ST398 lineage.
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Affiliation(s)
- Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB Groningen, the Netherlands
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Glasner C, Sabat AJ, Chlebowicz MA, Vanderhaeghen W, Fetsch A, Guerra B, Huber H, Stephan R, Torres C, Butaye P, Voss A, Wulf M, van Dijl JM. High-resolution typing by MLVF unveils extensive heterogeneity of European livestock-associated methicillin-resistant Staphylococcus aureus isolates with the sequence type 398. Int J Med Microbiol 2013; 303:124-7. [DOI: 10.1016/j.ijmm.2013.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/07/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022] Open
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Carriço JA, Sabat AJ, Friedrich AW, Ramirez M. Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution. ACTA ACUST UNITED AC 2013; 18:20382. [PMID: 23369390 DOI: 10.2807/ese.18.04.20382-en] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Advances in typing methodologies have been the driving force in the field of molecular epidemiology of pathogens. The development of molecular methodologies, and more recently of DNA sequencing methods to complement and improve phenotypic identification methods, was accompanied by the generation of large amounts of data and the need to develop ways of storing and analysing them. Simultaneously, advances in computing allowed the development of specialised algorithms for image analysis, data sharing and integration, and for mining the ever larger amounts of accumulated data. In this review, we will discuss how bioinformatics accompanied the changes in bacterial molecular epidemiology. We will discuss the benefits for public health of specialised online typing databases and algorithms allowing for real-time data analysis and visualisation. The impact of the new and disruptive next-generation sequencing methodologies will be evaluated, and we will look ahead into these novel challenges.
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Affiliation(s)
- J A Carriço
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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Sabat AJ, Budimir A, Nashev D, Sá-Leão R, van Dijl JM, Laurent F, Grundmann H, Friedrich AW. Overview of molecular typing methods for outbreak detection and epidemiological surveillance. ACTA ACUST UNITED AC 2013; 18:20380. [PMID: 23369389 DOI: 10.2807/ese.18.04.20380-en] [Citation(s) in RCA: 346] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages.
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Affiliation(s)
- A J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Wladyka B, Bista M, Sabat AJ, Bonar E, Grzeszczuk S, Hryniewicz W, Dubin A. A novel member of the thermolysin family, cloning and biochemical characterization of metalloprotease from Staphylococcus pseudintermedius. Acta Biochim Pol 2008; 55:525-536. [PMID: 18769737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Revised: 08/06/2008] [Accepted: 09/01/2008] [Indexed: 05/26/2023]
Abstract
Thermolysins constitute a family of secreted bacterial metalloproteases expressed, among others, by several pathogens. Strains of Staphylococcus pseudintermedius isolated from diseased dogs and judged as protease-positive, by skim milk agar plate culture, were investigated for protease content. No proteolytic activity was detected when the bacteria were grown in regular liquid media. Unexpectedly, supplementation of the medium with calcium ions resulted in expression of a metalloprotease and profound changes in the profile of extracellular proteins. On the basis of homology to other staphylococcal metalloproteases, the nucleotide sequence of the gene encoding this protease (Pst) and its flanking regions was determined. The full-length pst codes for a protein with an open reading frame of 505 amino acids. The internal region contains the HEXXH catalytic domain that is conserved in members of the thermolysin family. Regardless of the presence of calcium in the medium, the expression of the protease gene was of the same intensity. This suggests that regulation of the metalloprotease production by calcium ions is at a post-transcriptional level. Isolates of S. pseudintermedius exhibit a proteolytic phenotype due to the metalloprotease expression, however only in presence of calcium ions, which most probably stabilize the structure of the protease.
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Affiliation(s)
- Benedykt Wladyka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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Wladyka B, Bista M, Sabat AJ, Bonar E, Grzeszczuk S, Hryniewicz W, Dubin A. A novel member of the thermolysin family, cloning and biochemical characterization of metalloprotease from Staphylococcus pseudintermedius. Acta Biochim Pol 2008. [DOI: 10.18388/abp.2008_3059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thermolysins constitute a family of secreted bacterial metalloproteases expressed, among others, by several pathogens. Strains of Staphylococcus pseudintermedius isolated from diseased dogs and judged as protease-positive, by skim milk agar plate culture, were investigated for protease content. No proteolytic activity was detected when the bacteria were grown in regular liquid media. Unexpectedly, supplementation of the medium with calcium ions resulted in expression of a metalloprotease and profound changes in the profile of extracellular proteins. On the basis of homology to other staphylococcal metalloproteases, the nucleotide sequence of the gene encoding this protease (Pst) and its flanking regions was determined. The full-length pst codes for a protein with an open reading frame of 505 amino acids. The internal region contains the HEXXH catalytic domain that is conserved in members of the thermolysin family. Regardless of the presence of calcium in the medium, the expression of the protease gene was of the same intensity. This suggests that regulation of the metalloprotease production by calcium ions is at a post-transcriptional level. Isolates of S. pseudintermedius exhibit a proteolytic phenotype due to the metalloprotease expression, however only in presence of calcium ions, which most probably stabilize the structure of the protease.
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Karynski M, Sabat AJ, Empel J, Hryniewicz W. Molecular surveillance of methicillin-resistant Staphylococcus aureus by multiple-locus variable number tandem repeat fingerprinting (formerly multiple-locus variable number tandem repeat analysis) and spa typing in a hierarchic approach. Diagn Microbiol Infect Dis 2008; 62:255-62. [PMID: 18708278 DOI: 10.1016/j.diagmicrobio.2008.06.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 06/10/2008] [Accepted: 06/25/2008] [Indexed: 11/18/2022]
Abstract
In this study, clonal relatedness of 202 Staphylococcus aureus (mostly methicillin-resistant) isolates recovered in 29 Polish hospitals was investigated by multiple-locus variable number tandem repeat fingerprinting (MLVF) and spa typing. Our analysis yielded 69 MLVF patterns and 34 spa types. Almost all isolates (97.4%) identical by MLVF were also indistinguishable by spa typing. Therefore, the MLVF method can be a cheap and fast screen before spa typing. Moreover, results obtained by MLVF suggest a set of simple criteria for grouping of spa types. The proposed algorithm groups isolates into the same cluster when spa sequences differ by a single mutation event: i) a single deletion or insertion of repeat unit(s) at the X region of the protein A gene or ii) a single nucleotide polymorphism within a repeat sequence. The combined use of these 2 methods, MLVF in local laboratories and spa typing of selected isolates in reference centers, can improve the monitoring of hospital-to-hospital strain transmission events and public health interventions on a huge scale.
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Affiliation(s)
- Michal Karynski
- National Medicines Institute, Division of Clinical Microbiology and Infection Prevention, 00-725 Warsaw, Poland
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