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Romero LC, Silva LP, Teixeira NB, de Camargo KV, Del Masso Pereira MA, Corrente JE, Pereira VC, Ribeiro de Souza da Cunha MDL. Staphylococcus capitis Bloodstream Isolates: Investigation of Clonal Relationship, Resistance Profile, Virulence and Biofilm Formation. Antibiotics (Basel) 2024; 13:147. [PMID: 38391533 PMCID: PMC10885910 DOI: 10.3390/antibiotics13020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Staphylococcus capitis has been recognized as a relevant opportunistic pathogen, particularly its persistence in neonatal ICUs around the world. Therefore, the aim of this study was to describe the epidemiological profile of clinical isolates of S. capitis and to characterize the factors involved in the persistence and pathogenesis of these strains isolated from blood cultures collected in a hospital in the interior of the state of São Paulo, Brazil. A total of 141 S. capitis strains were submitted to detection of the mecA gene and SCCmec typing by multiplex PCR. Genes involved in biofilm production and genes encoding enterotoxins and hemolysins were detected by conventional PCR. Biofilm formation was evaluated by the polystyrene plate adherence test and phenotypic resistance was investigated by the disk diffusion method. Finally, pulsed-field gel electrophoresis (PFGE) was used to analyze the clonal relationship between isolates. The mecA gene was detected in 99 (70.2%) isolates, with this percentage reaching 100% in the neonatal ICU. SCCmec type III was the most prevalent type, detected in 31 (31.3%) isolates and co-occurrence of SCCmec was also observed. In vitro biofilm formation was detected in 46 (32.6%) isolates but was not correlated with the presence of the ica operon genes. Furthermore, biofilm production in ICU isolates was favored by hyperosmotic conditions, which are common in ICUs because of the frequent parenteral nutrition. Analysis of the clonal relationship between the isolates investigated in the present study confirms a homogeneous profile of S. capitis and the persistence of clones that are prevalent in the neonatal ICU and disseminated across the hospital. This study highlights the adaptation of isolates to specific hospital environments and their high clonality.
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Affiliation(s)
- Letícia Calixto Romero
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Lucas Porangaba Silva
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Nathalia Bibiana Teixeira
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Karen Vilegas de Camargo
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | | | - José Eduardo Corrente
- Department of Biostatistics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-900, Brazil
| | - Valéria Cataneli Pereira
- Microbiology Laboratory, Universidade do Oeste Paulista (UNOESTE), Presidente Prudente 18618-970, Brazil
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Szekat C, Josten M, Rickmeyer J, Crüsemann M, Bierbaum G. A Staphylococcus capitis strain with unusual bacteriocin production. Microb Biotechnol 2023; 16:2181-2193. [PMID: 37850940 PMCID: PMC10616647 DOI: 10.1111/1751-7915.14356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Staphylococcus capitis is a member of the human and mammal skin microbiomes and is considered less harmful than Staphylococcus aureus. S. capitis subsp. urealyticus BN2 was isolated from a cat and expressed strong antibacterial activity against a range of Gram-positive species, most notably including S. aureus strains with resistance to methicillin (MRSA) and strains with intermediate resistance to vancomycin (VISA). These latter strains are normally relatively resistant to bacteriocins, due to cell wall and cell membrane modifications. Genomic sequencing showed that the strain harboured at least two complete gene clusters for biosynthesis of antagonistic substances. The complete biosynthetic gene cluster of the well-known lantibiotic gallidermin was encoded on a large plasmid and the mature peptide was present in isopropanol cell extracts. In addition, a chromosomal island contained a novel non-ribosomal peptide synthetase (NRPS) gene cluster. Accidental deletion of two NRPS modules and partial purification of the anti-VISA activity showed that this novel bacteriocin represents a complex of differently decorated, non-ribosomal peptides. Additionally, a number of phenol-soluble modulins (PSMs) was detected by mass spectrometry of whole cells. Producing these compounds, the strain was able to outcompete several S. aureus strains, including MRSA and VISA, in tube cultures.
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Affiliation(s)
- Christiane Szekat
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Michaele Josten
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Jasmin Rickmeyer
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
| | - Max Crüsemann
- Institute of Pharmaceutical BiologyUniversity of BonnBonnGermany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and ParasitologyUniversity Hospital BonnBonnGermany
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3
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Field D, Fernandez de Ullivarri M, Ross RP, Hill C. After a century of nisin research - where are we now? FEMS Microbiol Rev 2023; 47:fuad023. [PMID: 37300874 PMCID: PMC10257480 DOI: 10.1093/femsre/fuad023] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023] Open
Abstract
It is almost a century since nisin was discovered in fermented milk cultures, coincidentally in the same year that penicillin was first described. Over the last 100 years this small, highly modified pentacyclic peptide has not only found success in the food industry as a preservative but has also served as the paradigm for our understanding of the genetic organization, expression, and regulation of genes involved in lantibiotic biosynthesis-one of the few cases of extensive post-translation modification in prokaryotes. Recent developments in understanding the complex biosynthesis of nisin have shed light on the cellular location of the modification and transport machinery and the co-ordinated series of spatio-temporal events required to produce active nisin and provide resistance and immunity. The continued unearthing of new natural variants from within human and animal gastrointestinal tracts has sparked interest in the potential application of nisin to influence the microbiome, given the growing recognition of the role the gastrointestinal microbiota plays in health and disease. Moreover, interdisciplinary approaches have taken advantage of biotechnological advancements to bioengineer nisin to produce novel variants and expand nisin functionality for applications in the biomedical field. This review will discuss the latest progress in these aspects of nisin research.
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Affiliation(s)
- Des Field
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
| | | | - R Paul Ross
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork,Western Road, Cork T12 YN60, Ireland
- School of Microbiology, University College Cork, College Road, Cork T12 YT20, Ireland
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4
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Chavignon M, Coignet L, Bonhomme M, Bergot M, Tristan A, Verhoeven P, Josse J, Laurent F, Butin M. Environmental Persistence of Staphylococcus capitis NRCS-A in Neonatal Intensive Care Units: Role of Biofilm Formation, Desiccation, and Disinfectant Tolerance. Microbiol Spectr 2022; 10:e0421522. [PMID: 36409142 PMCID: PMC9769769 DOI: 10.1128/spectrum.04215-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022] Open
Abstract
The clone Staphylococcus capitis NRCS-A is responsible for late-onset sepsis in neonatal intensive care units (NICUs) worldwide. Over time, this clone has evolved into three subgroups that are increasingly adapted to the NICU environment. This study aimed to decipher the mechanisms involved in NRCS-A persistence in NICUs. Twenty-six S. capitis strains belonging to each of the three NRCS-A clone subgroups and two other non-NRCS-A groups from neonates (alpha clone) or from adult patients ("other strains") were compared based on growth kinetics and ability to form biofilm as well as tolerance to desiccation and to different disinfectants. S. capitis biofilm formation was enhanced in rich medium and decreased under conditions of nutrient stress for all strains. However, under conditions of nutrient stress, NRCS-A strains presented an enhanced ability to adhere and form a thin biofilm containing more viable and culturable bacteria (mean 5.7 log10 CFU) than the strains from alpha clone (mean, 1.1 log10 CFU) and the "other strains" (mean, 4.2 log10 CFU) (P < 0.0001). The biofilm is composed of bacterial aggregates with a matrix mainly composed of polysaccharides. The NRCS-A clone also showed better persistence after a 48-h desiccation. However, disinfectant tolerance was not enhanced in the NRCS-A clone in comparison with that of strains from adult patients. In conclusion, the ability to form biofilm under nutrient stress and to survive desiccation are two major advantages for clone NRCS-A that could explain its ability to persist and settle in the specific environment of NICU settings. IMPORTANCE Neonatal intensive care units (NICUs) host extremely fragile newborns, including preterm neonates. These patients are very susceptible to nosocomial infections, with coagulase-negative staphylococci being the species most frequently involved. In particular, a Staphylococcus capitis clone named NRCS-A has emerged worldwide specifically in NICUs and is responsible for severe nosocomial sepsis in preterm neonates. This clone is specifically adapted to the NICU environment and is able to colonize and maintain on NICU surfaces. The present work explored the mechanisms involved in the persistence of the NRCS-A clone in the NICU environment despite strict hygiene measures. The ability to produce biofilm under nutritional stress and to resist desiccation appear to be the two main advantages of NRCS-A in comparison with other strains. These findings are pivotal to provide clues for subsequent development of targeted methods to combat NRCS-A and to stop its dissemination.
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Affiliation(s)
- Marie Chavignon
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Ludivine Coignet
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Mélanie Bonhomme
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Marine Bergot
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Anne Tristan
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Paul Verhoeven
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP (Groupe sur l’Immunité des Muqueuses et Agents Pathogènes), INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Jérôme Josse
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Frédéric Laurent
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Marine Butin
- Centre International de Recherche en Infectiologie (CIRI), Team Pathogénie des Staphylocoques, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS Lyon, Lyon, France
- Service de Néonatologie et Réanimation Néonatale, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France
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Genetic Characterization of Staphylococcus aureus, Staphylococcus argenteus, and Coagulase-Negative Staphylococci Colonizing Oral Cavity and Hand of Healthy Adults in Northern Japan. Pathogens 2022; 11:pathogens11080849. [PMID: 36014970 PMCID: PMC9413425 DOI: 10.3390/pathogens11080849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023] Open
Abstract
The spread of methicillin resistance and virulence among staphylococci in the community poses a public health concern. In this study, we investigated the prevalence of Staphylococcus species colonizing the oral cavity and hand (skin) of healthy university students and their phenotypic and genetic characteristics in northern Japan. Among a total of 332 subjects, 6 and 110 methicillin-resistant and susceptible Staphylococcus aureus (MRSA and MSSA, respectively) isolates were recovered from 105 subjects. MRSA isolates were genotyped as CC5, CC8, CC45, and CC59 with SCCmec-IIa or IV, among which an isolate of ST6562 (single-locus variant of ST8) harbored SCCmec-IVa, PVL genes and ACME-I, which are the same traits as the USA300 clone. ST1223 S. argenteus was isolated from the oral cavity and hand of a single student. Coagulase-negative Staphylococcus (CoNS) was recovered from 154 subjects (172 isolates), and classified into 17 species, with S. capitis being the most common (38%), followed by S. warneri (24%) and S. epidermidis (15%), including nine mecA-positive isolates. S. capitis was differentiated into seven clusters/subclusters, and genetic factors associated with the NRCS-A clone (nsr, tarJ, ebh) were detected in 10–21% of isolates. The colonization of the USA300-like MRSA variant and S. capitis with the traits of the NRCS-A clone in healthy individuals was noteworthy.
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Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol 2021; 19:726-739. [PMID: 34075213 DOI: 10.1038/s41579-021-00569-w] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.
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Affiliation(s)
- Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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7
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Tevell S, Baig S, Hellmark B, Martins Simoes P, Wirth T, Butin M, Nilsdotter-Augustinsson Å, Söderquist B, Stegger M. Presence of the neonatal Staphylococcus capitis outbreak clone (NRCS-A) in prosthetic joint infections. Sci Rep 2020; 10:22389. [PMID: 33372186 PMCID: PMC7769963 DOI: 10.1038/s41598-020-79225-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/03/2020] [Indexed: 11/28/2022] Open
Abstract
Staphylococcus capitis is a coagulase-negative staphylococcus that has been described primarily as causing bloodstream infections in neonatal intensive care units (NICUs), but has also recently been described in prosthetic joint infections (PJIs). The multidrug-resistant S. capitis subsp. urealyticus clone NRCS-A, comprising three sublineages, is prevalent in NICUs across the world, but its impact on other patient groups such as those suffering from PJIs or among adults planned for arthroplasty is unknown. Genome sequencing and subsequent analysis were performed on a Swedish collection of PJI isolates (n = 21), nasal commensals from patients planned to undergo arthroplasty (n = 20), NICU blood isolates (n = 9), operating theatre air isolates (n = 4), and reference strains (n = 2), in conjunction with an international strain collection (n = 248). The NRCS-A Outbreak sublineage containing the composite type V SCCmec-SCCcad/ars/cop element was present in PJIs across three Swedish hospitals. However, it was not found among nasal carrier strains, where the less virulent S. capitis subsp. capitis was most prevalent. The presence of the NRCS-A Outbreak clone in adult patients with PJIs demonstrates that dissemination occurs beyond NICUs. As this clone has several properties which facilitate invasive infections in patients with medical implants or immunosuppression, such as biofilm forming ability and multidrug resistance including heterogeneous glycopeptide-intermediate susceptibility, further research is needed to understand the reservoirs and distribution of this hospital-associated pathogen.
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Affiliation(s)
- Staffan Tevell
- Department of Infectious Diseases, Karlstad Hospital and Centre for Clinical Research and Education, Värmland County Council, SE-65182, Karlstad, Sweden. .,School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Sharmin Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bengt Hellmark
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Patricia Martins Simoes
- Department of Bacteriology, Institute for Infectious Agents, National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France.,Centre International de Référence en Infectiologie, INSERM U1111, CNRS UMR 5308, ENS, University of Lyon, Lyon, France
| | - Thierry Wirth
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR-CNRS 7205, Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Paris, France.,École Pratique des Hautes Études, PSL Université, Paris, France
| | - Marine Butin
- Centre International de Référence en Infectiologie, INSERM U1111, CNRS UMR 5308, ENS, University of Lyon, Lyon, France.,Neonatal Intensive Care Unit, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Lyon, France
| | - Åsa Nilsdotter-Augustinsson
- Division of Inflammation and Infection, Department of Infectious Diseases, Linköping University, Norrköping, Sweden.,Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Norrköping, Sweden
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marc Stegger
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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8
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Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis. Nat Microbiol 2020; 5:735-745. [PMID: 32341568 DOI: 10.1038/s41564-020-0676-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
The multidrug-resistant Staphylococcus capitis NRCS-A clone is responsible for sepsis in preterm infants in neonatal intensive care units (NICUs) worldwide. Here, to retrace the spread of this clone and to identify drivers of its specific success, we investigated a representative collection of 250 S. capitis isolates from adults and newborns. Bayesian analyses confirmed the spread of the NRCS-A clone and enabled us to date its emergence in the late 1960s and its expansion during the 1980s, coinciding with the establishment of NICUs and the increasing use of vancomycin in these units, respectively. This dynamic was accompanied by the acquisition of mutations in antimicrobial resistance- and bacteriocin-encoding genes. Furthermore, combined statistical tools and a genome-wide association study convergently point to vancomycin resistance as a major driver of NRCS-A success. We also identified another S. capitis subclade (alpha clade) that emerged independently, showing parallel evolution towards NICU specialization and non-susceptibility to vancomycin, indicating convergent evolution in NICU-associated pathogens. These findings illustrate how the broad use of antibiotics can repeatedly lead initially commensal drug-susceptible bacteria to evolve into multidrug-resistant clones that are able to successfully spread worldwide and become pathogenic for highly vulnerable patients.
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9
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Thorn LM, Ussher JE, Broadbent RS, Manning JM, Sharples KJ, Crump JA. Risk factors for Staphylococcus capitis pulsotype NRCS-A colonisation among premature neonates in the neonatal intensive care unit of a tertiary-care hospital: a retrospective case-control study. Infect Prev Pract 2020; 2:100057. [PMID: 34368703 PMCID: PMC8335916 DOI: 10.1016/j.infpip.2020.100057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/12/2020] [Indexed: 11/01/2022] Open
Abstract
Background A S. capitis strain called NRCS-A (S. capitis NRCS-A) has emerged as a cause of bloodstream infections and sepsis in neonatal intensive care units (NICUs) worldwide. Aim To identify risk factors for S. capitis NRCS-A colonisation among neonates, Dunedin Hospital NICU, Dunedin, New Zealand, from September 2013 through March 2015. Methods Weekly axillary swabs categorised eligible neonates as a case or a control. A case was defined as a week ending with a neonate's first positive swab for S. capitis NRCS-A and a control as a week in which a neonate remained negative. Weekly exposures were abstracted from hospital medical records. Analyses were performed using conditional logistic regression. Findings The median (range) gestational age at birth of participants was 32.7 (23.1-41.3) weeks. Participants contributed 26 weeks of case data and 177 weeks of control data. On adjusted analysis compared with matched controls, cases had higher odds of requiring invasive mechanical ventilation (OR 3.6, 95% CI: 1.1-11.6, p=0.035) and of a patent ductus arteriosus (PDA) (OR 3.0, 95% CI: 1.0-9.0, p=0.044). Cases had lower odds of being part of a multiple birth (OR 0.24, 95% CI 0.08-0.73, p=0.001), having an area of inflamed skin (OR 0.31, 95% CI: 0.13-0.75, p=0.009), and specifically an area of inflamed axillary skin (OR 0.08, 95% CI: 0.01-0.50, p=0.006). Conclusions We found that premature neonates with invasive mechanical ventilation and PDA had greater odds for S. capitis NRCS-A colonisation. Transmission may be mediated by increased staff contact, but prospective research is needed to confirm this.
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Affiliation(s)
- Louise M Thorn
- Department of Preventive and Social Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Southern Community Laboratories, Dunedin, New Zealand
| | - Roland S Broadbent
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.,Neonatal Intensive Care Unit, Dunedin Hospital, Dunedin, New Zealand
| | - Juliet M Manning
- Neonatal Intensive Care Unit, Dunedin Hospital, Dunedin, New Zealand
| | - Katrina J Sharples
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand.,Centre for International Health, University of Otago, New Zealand
| | - John A Crump
- Centre for International Health, University of Otago, New Zealand
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10
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O'Sullivan JN, O'Connor PM, Rea MC, O'Sullivan O, Walsh CJ, Healy B, Mathur H, Field D, Hill C, Ross RP. Nisin J, a Novel Natural Nisin Variant, Is Produced by Staphylococcus capitis Sourced from the Human Skin Microbiota. J Bacteriol 2020; 202:e00639-19. [PMID: 31740495 PMCID: PMC6964739 DOI: 10.1128/jb.00639-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/05/2019] [Indexed: 02/04/2023] Open
Abstract
The skin microbiota is thought to play a key role in host protection from infection. Nisin J is a novel nisin variant produced by Staphylococcus capitis APC 2923, a strain isolated from the toe web space area in a screening study performed on the human skin microbiota. Whole-genome sequencing and mass spectrometry of the purified peptide confirmed that S. capitis APC 2923 produces a 3,458-Da bacteriocin, designated nisin J, which exhibited antimicrobial activity against a range of Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) and Cutibacterium acnes The gene order in the nisin J gene cluster (nsjFEGBTCJP) differs from that of other nisin variants in that it is lacking the nisin regulatory genes, nisRK, as well as the nisin immunity gene nisI Nisin J has 9 amino acid changes compared to prototypical nisin A, with 8 amino acid substitutions, 6 of which are not present in other nisin variants (Ile4Lys, Met17Gln, Gly18Thr, Asn20Phe, Met21Ala, Ile30Gly, Val33His, and Lys34Thr), and an extra amino acid close to the C terminus, rendering nisin J the only nisin variant to contain 35 amino acids. This is the first report of a nisin variant produced by a Staphylococcus species and the first nisin producer isolated from human skin.IMPORTANCE This study describes the characterization of nisin J, the first example of a natural nisin variant, produced by a human skin isolate of staphylococcal origin. Nisin J displays inhibitory activity against a wide range of bacterial targets, including MRSA. This work demonstrates the potential of human commensals as a source for novel antimicrobials that could form part of the solution to antibiotic resistance across a broad range of bacterial pathogens.
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Affiliation(s)
- Julie N O'Sullivan
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paula M O'Connor
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mary C Rea
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Brian Healy
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Harsh Mathur
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Des Field
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - R Paul Ross
- Teagasc Food Research Centre, Fermoy, County Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Complete genome and bimodal genomic structure of the amoebal symbiont Neochlamydia strain S13 revealed by ultra-long reads obtained from MinION. J Hum Genet 2019; 65:41-48. [PMID: 31723216 DOI: 10.1038/s10038-019-0684-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022]
Abstract
Neochlamydia strain S13 is an amoebal symbiont of an Acanthamoeba sp. The symbiont confers resistance to Legionella pneumophila on its host; however, the molecular mechanism underlying this resistance is not completely understood. Genome analyses have been crucial for understanding the complicated host-symbiont relationship but segregating the host's genome DNA from the symbiont's DNA is often challenging. In this study, we successfully identified a bimodal genomic structure in Neochlamydia strain S13 using PacBio RS II supported by ultra-long reads derived from MinION. One mode consisted of circular sequences of 2,586,667 and 231,307 bp; the other was an integrated sequence of the two via long homologous regions. They encoded 2175 protein-coding regions, some of which were implied to be acquired via horizontal gene transfer. They were specifically conserved in the genus Neochlamydia and formed a cluster in the genome, presumably by multiplication through genome replication. Moreover, it was notable that the sequenced DNA was obtained without segregating the symbiont DNA from the host. This is an easy and versatile technique that facilitates the characterization of diverse hosts and symbionts in nature.
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12
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Genomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden. Eur J Clin Microbiol Infect Dis 2019; 38:2069-2075. [PMID: 31396832 PMCID: PMC6800862 DOI: 10.1007/s10096-019-03647-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/15/2019] [Indexed: 12/04/2022]
Abstract
Emergence of a genetically distinct, multidrug-resistant Staphylococcus capitis clone (NRCS-A) present in neonatal intensive care units has recently been extensively reported. The aims of the present study were to investigate which clones of S. capitis isolated from blood in a Swedish neonatal intensive care unit (NICU) have been present since 1987 and to investigate whether the NRCS-A clone has disseminated in Sweden. All S. capitis isolates from blood cultures of neonates (≤ 28 days of age) between 1987 and 2017 (n = 46) were whole-genome sequenced, and core genome multilocus sequence typing (cgMLST) was performed. Single-nucleotide polymorphism (SNP)-based phylogenetic relationships between the S. capitis isolates and in silico predictions of presence of genetic traits specific to the NRCS-A clone were identified. Furthermore, antibiotic susceptibility testing, including screening for heterogeneous glycopeptide-intermediate resistance, was performed. Thirty-five isolates clustered closely to the isolates previously determined as belonging to the NRCS-A clone and had fewer than 81 core genome loci differences out of 1063. Twenty-one of these isolates were multidrug resistant. The NRCS-A clone was found in 2001. Six pairs of isolates had differences of fewer than two SNPs. Genetic traits associated with the NRCS-A clone such as nsr, ebh, tarJ, and CRISPR were found in all 35 isolates. The increasing incidence of S. capitis blood cultures of neonates is predominantly represented by the NRSC-A clone at our NICU in Sweden. Furthermore, there were indications of transmission between cases; adherence to basic hygiene procedures and surveillance measures are thus warranted.
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13
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Ory J, Cazaban M, Richaud-Morel B, Di Maio M, Dunyach-Remy C, Pantel A, Sotto A, Laurent F, Lavigne JP, Butin M. Successful implementation of infection control measure in a neonatal intensive care unit to combat the spread of pathogenic multidrug resistant Staphylococcus capitis. Antimicrob Resist Infect Control 2019; 8:57. [PMID: 30962919 PMCID: PMC6437968 DOI: 10.1186/s13756-019-0512-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/19/2019] [Indexed: 11/10/2022] Open
Abstract
Background Once present in a neonatal intensive care unit (NICU), multidrug resistant Staphylococcus capitis NRCS-A is able to settle and diffuse. Objective The objective of this study was to evaluate the impact of infection control (IC) interventions to reduce the spread of Staphylococcus capitis NRCS-A in a NICU. Methods Between December 2012 and December 2017, all patients presenting positive sampling (blood, skin or catheter) to S. capitis were included, and clinical data were recorded from electronic clinical charts. The IC team has continually implemented measures of control infections (hand hygiene, standard precautions, patient contact isolation and disinfection of the inanimate environment). From May 2015, a steam cleaner was implemented in the cleaning procedure instead of disinfectant to disinfect heating tables and incubators. Four periods were determined: Period 1 (P1) before steam cleaner acquisition; Period 2 (P2) after implementation steam cleaner; Period 3 (P3) when the steam cleaner had broken down, and Period 4 (P4) when the steam cleaner was functional again. The consumption of antibiotics and the epidemiology of infections inside the NICU were investigated during the study period. Results During the studied period, 37 infants were infected or colonized by S. capitis. The incidences of infection or colonization by S. capitis were P1 = 1.04‰, P2 = 0.55‰, P3 = 3.95 ‰ and P4 = 0‰ and were significantly different between P1-P3 and P2-P4 (p < 0.001). During the different periods, antibiotics consumption and bacterial epidemiology of the ward were stable. Conclusions The use of steam vapor system was associated with a significantly decreased incidence of S. capitis NRCS-A infection or colonization and could constitute an effective and safe procedure to control and eradicate its diffusion inside NICUs.
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Affiliation(s)
- Jérôme Ory
- 1Department of Infection Control, Equipe Opérationnelle d'Hygiène, Place du Professeur Robert Debré, University Hospital Nîmes, Nîmes, France
| | - Michel Cazaban
- 1Department of Infection Control, Equipe Opérationnelle d'Hygiène, Place du Professeur Robert Debré, University Hospital Nîmes, Nîmes, France
| | - Brigitte Richaud-Morel
- 1Department of Infection Control, Equipe Opérationnelle d'Hygiène, Place du Professeur Robert Debré, University Hospital Nîmes, Nîmes, France
| | - Massimo Di Maio
- 2Department of Neonatalogy, University Hospital Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- 3Bacterial virulence and Infectious Diseases, INSERM, Department of Microbiology, Université de Montpellier, University Hospital Nîmes, Nîmes cedex 02, 30908 Nîmes, France
| | - Alix Pantel
- 3Bacterial virulence and Infectious Diseases, INSERM, Department of Microbiology, Université de Montpellier, University Hospital Nîmes, Nîmes cedex 02, 30908 Nîmes, France
| | - Albert Sotto
- 4Department of Infectious Diseases, Bacterial virulence and Infectious Diseases, INSERM, Université de Montpellier, University Hospital Nîmes, Nîmes, France
| | - Frédéric Laurent
- 5International Center of Research in Infectiology, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure, Lyon, France.,Institute of Infectious Agents, Lyon, France.,National Reference Center for Staphylococci, Lyon, France.,8Department of Microbiology-Mycology, Institut des Sciences Pharmaceutiques et Biologiques de Lyon, University of Lyon, Lyon, France
| | - Jean-Philippe Lavigne
- 3Bacterial virulence and Infectious Diseases, INSERM, Department of Microbiology, Université de Montpellier, University Hospital Nîmes, Nîmes cedex 02, 30908 Nîmes, France
| | - Marine Butin
- 5International Center of Research in Infectiology, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure, Lyon, France.,Institute of Infectious Agents, Lyon, France.,National Reference Center for Staphylococci, Lyon, France.,8Department of Microbiology-Mycology, Institut des Sciences Pharmaceutiques et Biologiques de Lyon, University of Lyon, Lyon, France
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Laurent F, Butin M. Staphylococcus capitis and NRCS-A clone: the story of an unrecognized pathogen in neonatal intensive care units. Clin Microbiol Infect 2019; 25:1081-1085. [PMID: 30928561 DOI: 10.1016/j.cmi.2019.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/07/2019] [Accepted: 03/09/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND In neonatal intensive care units (NICUs), nosocomial late-onset sepsis (LOS), mostly due to coagulase negative staphylococci, constitute a major cause of death or impairment. Staphylococcus capitis, usually considered as a poorly virulent species, has been reported as a cause of LOS. OBJECTIVES To review data regarding S. capitis neonatal LOS and the features of isolates involved. SOURCES PubMed was searched up to August 2018 to retrieve studies on the topic; the keywords used were 'S. capitis', 'neonate', 'neonatal ICU', 'bloodstream infection' and 'late onset sepsis'. CONTENT Published data highlight the worldwide endemicity of a single S. capitis clone, named NRCS-A, specifically involved in LOS. NRCS-A harbours a multidrug resistance profile (including resistance to the usual first-line antibiotics used in NICUs). It is also able to adapt under vancomycin selective pressure that could confer an advantage for its implantation and dissemination in NICUs where this selective pressure is high. Moreover, a severe morbidity has been observed in NRCS-A-related LOS. The NICU environment, and especially incubators, constitute reservoirs of NRCS-A from which it could diffuse inside the setting. Finally, the virulome and resistome of S. capitis NRCS-A contain many genes potentially implicated in its specific epidemiology and pathophysiology, including the gene nsr that may be involved in its fitness and implantation in neonatal gut flora. IMPLICATIONS S. capitis must be considered as a true pathogen in neonates. The decreased susceptibility to vancomycin may be involved in failure of vancomycin therapy. Further studies are needed to better manage its diffusion inside each NICU but also worldwide.
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Affiliation(s)
- F Laurent
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 Allée d'Italie 69364 Lyon Cedex 07, France; Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, 103 Grande Rue de La Croix Rousse, 69004 Lyon, France; Département de Microbiologie et Mycologie, Institut des Sciences Pharmaceutiques et Biologiques de Lyon, Université de Lyon, 6 Avenue Rockefeller, 69008 Lyon, France
| | - M Butin
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 Allée d'Italie 69364 Lyon Cedex 07, France; Réanimation Néonatale, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 59 Bd Pinel 69500 Bron, France.
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Coagulase-Negative Staphylococci Pathogenomics. Int J Mol Sci 2019; 20:ijms20051215. [PMID: 30862021 PMCID: PMC6429511 DOI: 10.3390/ijms20051215] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/16/2023] Open
Abstract
Coagulase-negative Staphylococci (CoNS) are skin commensal bacteria. Besides their role in maintaining homeostasis, CoNS have emerged as major pathogens in nosocomial settings. Several studies have investigated the molecular basis for this emergence and identified multiple putative virulence factors with regards to Staphylococcus aureus pathogenicity. In the last decade, numerous CoNS whole-genome sequences have been released, leading to the identification of numerous putative virulence factors. Koch’s postulates and the molecular rendition of these postulates, established by Stanley Falkow in 1988, do not explain the microbial pathogenicity of CoNS. However, whole-genome sequence data has shed new light on CoNS pathogenicity. In this review, we analyzed the contribution of genomics in defining CoNS virulence, focusing on the most frequent and pathogenic CoNS species: S. epidermidis, S. haemolyticus, S. saprophyticus, S. capitis, and S. lugdunensis.
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Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis. Antimicrob Agents Chemother 2018; 62:AAC.00898-18. [PMID: 30150477 PMCID: PMC6201123 DOI: 10.1128/aac.00898-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/18/2018] [Indexed: 12/29/2022] Open
Abstract
Coagulase-negative staphylococci (CoNS), such as Staphylococcus capitis, are major causes of bloodstream infections in neonatal intensive care units (NICUs). Recently, a distinct clone of S. capitis (designated S. capitis NRCS-A) has emerged as an important pathogen in NICUs internationally. Coagulase-negative staphylococci (CoNS), such as Staphylococcus capitis, are major causes of bloodstream infections in neonatal intensive care units (NICUs). Recently, a distinct clone of S. capitis (designated S. capitis NRCS-A) has emerged as an important pathogen in NICUs internationally. Here, 122 S. capitis isolates from New Zealand (NZ) underwent whole-genome sequencing (WGS), and these data were supplemented with publicly available S. capitis sequence reads. Phylogenetic and comparative genomic analyses were performed, as were phenotypic assessments of antimicrobial resistance, biofilm formation, and plasmid segregational stability on representative isolates. A distinct lineage of S. capitis was identified in NZ associated with neonates and the NICU environment. Isolates from this lineage produced increased levels of biofilm, displayed higher levels of tolerance to chlorhexidine, and were multidrug resistant. Although similar to globally circulating NICU-associated S. capitis strains at a core-genome level, NZ NICU S. capitis isolates carried a novel stably maintained multidrug-resistant plasmid that was not present in non-NICU isolates. Neonatal blood culture isolates were indistinguishable from environmental S. capitis isolates found on fomites, such as stethoscopes and neonatal incubators, but were generally distinct from those isolates carried by NICU staff. This work implicates the NICU environment as a potential reservoir for neonatal sepsis caused by S. capitis and highlights the capacity of genomics-based tracking and surveillance to inform future hospital infection control practices aimed at containing the spread of this important neonatal pathogen.
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