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Bogut A, Koper P, Marczak M, Całka P. The first genomic characterization of a stable, hemin-dependent small colony variant strain of Staphylococcus epidermidis isolated from a prosthetic-joint infection. Front Microbiol 2023; 14:1289844. [PMID: 37928677 PMCID: PMC10620731 DOI: 10.3389/fmicb.2023.1289844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023] Open
Abstract
Phenotype switching from a wild type (WT) to a slow-growing subpopulation, referred to as small colony variants (SCVs), supports an infectious lifestyle of Staphylococcus epidermidis, the leading cause of medical device-related infections. Specific mechanisms underlying formation of SCVs and involved in the shaping of their pathogenic potential are of particular interest for stable strains as they have been only rarely cultured from clinical specimens. As the SCV phenotype stability implies the existence of genetic changes, the whole genome sequence of a stable, hemin-dependent S. epidermidis SCV strain (named 49SCV) involved in a late prosthetic joint infection was analyzed. The strain was isolated in a monoculture without a corresponding WT clone, therefore, its genome was compared against five reference S. epidermidis strains (ATCC12228, ATCC14990, NBRC113846, O47, and RP62A), both at the level of the genome structure and coding sequences. According to the Multilocus Sequence Typing analysis, the 49SCV strain represented the sequence type 2 (ST2) regarded as the most prominent infection-causing lineage with a worldwide dissemination. Genomic features unique to 49SCV included the absence of the Staphylococcal Cassette Chromosome (SCC), ~12 kb deletion with the loss of genes involved in the arginine deiminase pathway, and frameshift-generating mutations within the poly(A) and poly(T) homopolymeric tracts. Indels were identified in loci associated with adherence, metabolism, stress response, virulence, and cell wall synthesis. Of note, deletion in the poly(A) of the hemA gene has been considered a possible trigger factor for the phenotype transition and hemin auxotrophy in the strain. To our knowledge, the study represents the first genomic characterization of a clinical, stable and hemin-dependent S. epidermidis SCV strain. We propose that previously unreported indels in the homopolymeric tracts can constitute a background of the SCV phenotype due to a resulting truncation of the corresponding proteins and their possible biological dysfunction. Streamline of genetic content evidenced by the loss of the SCC and a large genomic deletion can represent a possible strategy associated both with the SCV phenotype and its adaptation to chronicity.
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Affiliation(s)
- Agnieszka Bogut
- Chair and Department of Medical Microbiology, Medical University of Lublin, Lublin, Poland
| | - Piotr Koper
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Małgorzata Marczak
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Paulina Całka
- Chair and Department of Forensic Medicine, Medical University of Lublin, Lublin, Poland
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Staphylococcus epidermidis and its dual lifestyle in skin health and infection. Nat Rev Microbiol 2023; 21:97-111. [PMID: 36042296 PMCID: PMC9903335 DOI: 10.1038/s41579-022-00780-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 01/20/2023]
Abstract
The coagulase-negative bacterium Staphylococcus epidermidis is a member of the human skin microbiota. S. epidermidis is not merely a passive resident on skin but actively primes the cutaneous immune response, maintains skin homeostasis and prevents opportunistic pathogens from causing disease via colonization resistance. However, it is now appreciated that S. epidermidis and its interactions with the host exist on a spectrum of potential pathogenicity derived from its high strain-level heterogeneity. S. epidermidis is the most common cause of implant-associated infections and is a canonical opportunistic biofilm former. Additional emerging evidence suggests that some strains of S. epidermidis may contribute to the pathogenesis of common skin diseases. Here, we highlight new developments in our understanding of S. epidermidis strain diversity, skin colonization dynamics and its multifaceted interactions with the host and other members of the skin microbiota.
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Lu Y, Cai WJ, Ren Z, Han P. The Role of Staphylococcal Biofilm on the Surface of Implants in Orthopedic Infection. Microorganisms 2022; 10:1909. [PMID: 36296183 PMCID: PMC9612000 DOI: 10.3390/microorganisms10101909] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/11/2022] [Accepted: 09/20/2022] [Indexed: 08/27/2023] Open
Abstract
Despite advanced implant sterilization and aseptic surgical techniques, implant-associated infection remains a major challenge for orthopedic surgeries. The subject of bacterial biofilms is receiving increasing attention, probably as a result of the wide acknowledgement of the ubiquity of biofilms in the clinical environment, as well as the extreme difficulty in eradicating them. Biofilm can be defined as a structured microbial community of cells that are attached to a substratum and embedded in a matrix of extracellular polymeric substances (EPS) that they have produced. Biofilm development has been proposed as occurring in a multi-step process: (i) attachment and adherence, (ii) accumulation/maturation due to cellular aggregation and EPS production, and (iii) biofilm detachment (also called dispersal) of bacterial cells. In all these stages, characteristic proteinaceous and non-proteinaceous compounds are expressed, and their expression is strictly controlled. Bacterial biofilm formation around implants shelters the bacteria and encourages the persistence of infection, which could lead to implant failure and osteomyelitis. These complications need to be treated by major revision surgeries and extended antibiotic therapies, which could lead to high treatment costs and even increase mortality. Effective preventive and therapeutic measures to reduce risks for implant-associated infections are thus in urgent need.
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Affiliation(s)
| | | | | | - Pei Han
- Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Azara E, Longheu CM, Attene S, Sanna S, Sale M, Addis MF, Tola S. Comparative profiling of agr locus, virulence, and biofilm-production genes of human and ovine non-aureus staphylococci. BMC Vet Res 2022; 18:212. [PMID: 35655210 PMCID: PMC9161600 DOI: 10.1186/s12917-022-03257-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background In a collaboration between animal and human health care professionals, we assessed the genetic characteristics shared by non-aureus staphylococci (NAS) infecting humans and dairy ewes to investigate their relatedness in a region concentrating half of the total National sheep stock. We examined by PCR 125 ovine and 70 human NAS for biofilm production, pyrogenic toxins, adhesins, autolysins genes, and accessory gene regulator (agr) locus. The microtiter plate assay (MPA) was used for the phenotypic screening of biofilm production. Ovine NAS included S. epidermidis, S. chromogenes, S. haemolyticus, S. simulans, S. caprae, S. warneri, S. saprophyticus, S. intermedius, and S. muscae. Human NAS included S. haemolyticus, S. epidermidis, S. hominis, S. lugdunensis, S. capitis, S. warneri, S. xylosus, S. pasteuri, and S. saprophyticus subsp. bovis. Results Phenotypically, 41 (32.8%) ovine and 24 (34.3%) human isolates were characterized as biofilm producers. Of the ovine isolates, 12 were classified as biofilm-producing while the remaining 29 as weak biofilm-producing. All 24 human isolates were considered weak biofilm-producing. Few S. epidermidis isolates harbored the icaA/D genes coding for the polysaccharide intercellular adhesin (PIA), while the bhp, aap, and embp genes coding biofilm accumulation proteins were present in both non-producing and biofilm-producing isolates. Fifty-nine sheep NAS (all S. epidermidis, 1 S. chromogenes, and 1 S. haemolyticus) and 27 human NAS (all S. epidermidis and 1 S. warneri) were positive for the agr locus: agr-3se (57.8%) followed by agr-1se (36.8%) predominated in sheep, while agr-1se (65.4%), followed by agr-2se (34.6%) predominated in humans. Concerning virulence genes, 40, 39.2, 47.2%, 52.8, 80 and 43.2% of the sheep isolates carried atlE, aae, sdrF, sdrG, eno and epbS respectively, against 37.1, 42.8, 32.8, 60, 100 and 100% of human isolates. Enterotoxins and tsst were not detected. Conclusions Considerable variation in biofilm formation ability was observed among NAS isolates from ovine and human samples. S. epidermidis was the best biofilm producer with the highest prevalence of adhesin-encoding genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03257-w.
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ALBA MARYILORENASEGURA, DURÁN-RODRIGUEZ ANDREATATIANA, PULIDO LUZMARYSALAZAR, ESCOBAR-PÉREZ JAVIER, GUTIÉRREZ SERGIOALEJANDRO, OSPINA JEANNETTENAVARRETE, BERMÚDEZ GLADYSPINILLA, MOLINA LILIANACONSTANZAMUÑOZ. Peptides DLL37-1 and LL37-1, an alternative to inhibit biofilm formation in clinical isolates of Staphylococcus aureus and Staphylococcus epidermidis. AN ACAD BRAS CIENC 2022; 94:e20210848. [DOI: 10.1590/0001-3765202220210848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/08/2021] [Indexed: 11/09/2022] Open
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Baquero F, Saralegui C, Marcos-Mencía D, Ballestero L, Vañó-Galván S, Moreno-Arrones ÓM, Del Campo R. Epidermis as a Platform for Bacterial Transmission. Front Immunol 2021; 12:774018. [PMID: 34925344 PMCID: PMC8671829 DOI: 10.3389/fimmu.2021.774018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
The epidermis constitutes a continuous external layer covering the body, offering protection against bacteria, the most abundant living organisms that come into contact with this barrier. The epidermis is heavily colonized by commensal bacterial organisms that help protect against pathogenic bacteria. The highly regulated and dynamic interaction between the epidermis and commensals involves the host’s production of nutritional factors promoting bacterial growth together to chemical and immunological bacterial inhibitors. Signal trafficking ensures the system’s homeostasis; conditions that favor colonization by pathogens frequently foster commensal growth, thereby increasing the bacterial population size and inducing the skin’s antibacterial response, eliminating the pathogens and re-establishing the normal density of commensals. The microecological conditions of the epidermis favors Gram-positive organisms and are unsuitable for long-term Gram-negative colonization. However, the epidermis acts as the most important host-to-host transmission platform for bacteria, including those that colonize human mucous membranes. Bacteria are frequently shared by relatives, partners, and coworkers. The epidermal bacterial transmission platform of healthcare workers and visitors can contaminate hospitalized patients, eventually contributing to cross-infections. Epidermal transmission occurs mostly via the hands and particularly through fingers. The three-dimensional physical structure of the epidermis, particularly the fingertips, which have frictional ridges, multiplies the possibilities for bacterial adhesion and release. Research into the biology of bacterial transmission via the hands is still in its infancy; however, tribology, the science of interacting surfaces in relative motion, including friction, wear and lubrication, will certainly be an important part of it. Experiments on finger-to-finger transmission of microorganisms have shown significant interindividual differences in the ability to transmit microorganisms, presumably due to genetics, age, sex, and the gland density, which determines the physical, chemical, adhesive, nutritional, and immunological status of the epidermal surface. These studies are needed to optimize interventions and strategies for preventing the hand transmission of microorganisms.
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Affiliation(s)
- Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Daniel Marcos-Mencía
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Luna Ballestero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Sergio Vañó-Galván
- Servicio de Dermatología, Hospital Universitario Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Universidad de Alcalá, Madrid, Spain
| | - Óscar M Moreno-Arrones
- Servicio de Dermatología, Hospital Universitario Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Universidad de Alcalá, Madrid, Spain
| | - Rosa Del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Department of Health Sciences, Universidad Alfonso X El Sabio, Madrid, Spain.,Centro de Investigación en Red en Enfermedades Infecciosas (CIBER-EEII), Madrid, Spain
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Yu B, Kong D, Cheng C, Xiang D, Cao L, Liu Y, He Y. Assembly and recognition of keratins: A structural perspective. Semin Cell Dev Biol 2021; 128:80-89. [PMID: 34654627 DOI: 10.1016/j.semcdb.2021.09.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 12/21/2022]
Abstract
Keratins are one of the major components of cytoskeletal network and assemble into fibrous structures named intermediate filaments (IFs), which are important for maintaining the mechanical properties of cells and tissues. Over the past decades, evidence has shown that the functions of keratins go beyond providing mechanical support for cells, they interact with multiple cellular components and are widely involved in the pathways of cell proliferation, differentiation, motility and death. However, the structural details of keratins and IFs are largely missing and many questions remain regarding the mechanisms of keratin assembly and recognition. Here we briefly review the current structural models and assembly of keratins as well as the interactions of keratins with the binding partners, which may provide a structural view for understanding the mechanisms of keratins in the biological activities and the related diseases.
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Affiliation(s)
- Bowen Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Immunology, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Dandan Kong
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Cheng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongxi Xiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Longxing Cao
- School of Life Science, Westlake University, Hangzhou, Zhejiang, China
| | - Yingbin Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongning He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Biliary-Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
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Glycan-Dependent Corneocyte Adherence of Staphylococcus epidermidis Mediated by the Lectin Subdomain of Aap. mBio 2021; 12:e0290820. [PMID: 34253065 PMCID: PMC8406310 DOI: 10.1128/mbio.02908-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Staphylococcus epidermidis and other coagulase-negative staphylococci (CoNS) that colonize skin are known to promote skin immunity and inhibit colonization of pathogens that cause skin and soft tissue infections, including Staphylococcus aureus. However, S. epidermidis adherence to corneocytes, the cells that constitute the uppermost layer of the skin epidermis, remains poorly understood. Our study documents that S. epidermidis corneocyte adherence is dependent upon the accumulation-associated protein (Aap). Aap is composed of two distinct A and B domains. The A domain is comprised of a repeat region and a conserved L-type lectin domain, whereas the fibrillar B domain, which is comprised of G5 and E repeats, is linked to the cell wall in a sortase-dependent manner. Our studies revealed that adherence to corneocytes is dependent upon the lectin subdomain within the A domain. However, significant adherence was only observed when the lectin domain was expressed with both the A repeat and the B domain, suggesting further interactions between these three domains. Our data also suggest that the A repeat domain is important for stability or expression of Aap. Deglycosylation treatment suggested that glycans expressed in the host stratum corneum serve as potential binding partners for Aap-mediated corneocyte adherence. Last, bioinformatic analyses of the predominant commensal species of CoNS identified open reading frames (ORFs) homologous to aap, thus suggesting that Aap orthologues containing lectin-like domains may provide the basis for staphylococcal colonization of skin. Corroborating these observations, adherence to corneocytes in an S. aureus mgrA mutant was dependent upon SasG, the Aap orthologue in S. aureus. IMPORTANCE Staphylococcus aureus is the most significant cause of skin and soft tissue infections yet it rarely colonizes the skin of healthy individuals. This is believed to be due, in part, to inhibition of colonization via toxic substances produced by normal skin flora, including by S. epidermidis. Furthermore, we surmise that S. aureus colonization inhibition may also be due to competition for binding sites on host corneocytes. To understand these potential interactions between S. aureus and S. epidermidis and, potentially, other coagulase-negative staphylococci, we must first understand how staphylococci adhere to corneocytes. This work documents that S. epidermidis adherence to corneocytes is dependent upon the fibrillar cell wall-associated protein Aap. Our work further documents that Aap binds to glycans exposed on the corneocyte surface, which are commonly exploited by bacteria to facilitate adherence to host cells. Furthermore, we find that Aap orthologues may be responsible for corneocyte adherence in other staphylococci, including in S. aureus.
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Pang S, Daley DA, Sahibzada S, Mowlaboccus S, Stegger M, Coombs GW. Genome-wide association studies reveal candidate genes associated to bacteraemia caused by ST93-IV CA-MRSA. BMC Genomics 2021; 22:418. [PMID: 34090342 PMCID: PMC8180019 DOI: 10.1186/s12864-021-07738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 05/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The global emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has seen the dominance of specific clones in different regions around the world with the PVL-positive ST93-IV as the predominant CA-MRSA clone in Australia. In this study we applied a genome-wide association study (GWAS) approach on a collection of Australian ST93-IV MRSA genomes to screen for genetic traits that might have assisted the ongoing transmission of ST93-IV in Australia. We also compared the genomes of ST93-IV bacteraemia and non-bacteraemia isolates to search for potential virulence genes associated with bacteraemia. RESULTS Based on single nucleotide polymorphism phylogenetics we revealed two distinct ST93-IV clades circulating concurrently in Australia. One of the clades contained isolates primarily isolated in the northern regions of Australia whilst isolates in the second clade were distributed across the country. Analyses of the ST93-IV genome plasticity over a 15-year period (2002-2017) revealed an observed gain in accessory genes amongst the clone's population. GWAS analysis on the bacteraemia isolates identified two gene candidates that have previously been associated to this kind of infection. CONCLUSIONS Although this hypothesis was not tested here, it is possible that the emergence of a ST93-IV clade containing additional virulence genes might be related to the high prevalence of ST93-IV infections amongst the indigenous population living in the northern regions of Australia. More importantly, our data also demonstrated that GWAS can reveal candidate genes for further investigations on the pathogenesis and evolution of MRSA strains within a same lineage.
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Affiliation(s)
- Stanley Pang
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia.
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia.
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance (AGAR), Fiona Stanley Hospital, Murdoch, Australia
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Marc Stegger
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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VanAken SM, Newton D, VanEpps JS. Improved diagnostic prediction of the pathogenicity of bloodstream isolates of Staphylococcus epidermidis. PLoS One 2021; 16:e0241457. [PMID: 33770084 PMCID: PMC7997010 DOI: 10.1371/journal.pone.0241457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/27/2021] [Indexed: 12/27/2022] Open
Abstract
With an estimated 440,000 active cases occurring each year, medical device associated infections pose a significant burden on the US healthcare system, costing about $9.8 billion in 2013. Staphylococcus epidermidis is the most common cause of these device-associated infections, which typically involve isolates that are multi-drug resistant and possess multiple virulence factors. S. epidermidis is also frequently a benign contaminant of otherwise sterile blood cultures. Therefore, tests that distinguish pathogenic from non-pathogenic isolates would improve the accuracy of diagnosis and prevent overuse/misuse of antibiotics. Attempts to use multi-locus sequence typing (MLST) with machine learning for this purpose had poor accuracy (~73%). In this study we sought to improve the diagnostic accuracy of predicting pathogenicity by focusing on phenotypic markers (i.e., antibiotic resistance, growth fitness in human plasma, and biofilm forming capacity) and the presence of specific virulence genes (i.e., mecA, ses1, and sdrF). Commensal isolates from healthy individuals (n = 23), blood culture contaminants (n = 21), and pathogenic isolates considered true bacteremia (n = 54) were used. Multiple machine learning approaches were applied to characterize strains as pathogenic vs non-pathogenic. The combination of phenotypic markers and virulence genes improved the diagnostic accuracy to 82.4% (sensitivity: 84.9% and specificity: 80.9%). Oxacillin resistance was the most important variable followed by growth rate in plasma. This work shows promise for the addition of phenotypic testing in clinical diagnostic applications.
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Affiliation(s)
- Shannon M. VanAken
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, United States of America
| | - Duane Newton
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - J. Scott VanEpps
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, United States of America
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States of America
- Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, United States of America
- Michigan Center for Integrative Research in Critical Care, University of Michigan, Ann Arbor, MI, United States of America
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, United States of America
- * E-mail:
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França A, Gaio V, Lopes N, Melo LDR. Virulence Factors in Coagulase-Negative Staphylococci. Pathogens 2021; 10:170. [PMID: 33557202 PMCID: PMC7913919 DOI: 10.3390/pathogens10020170] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Coagulase-negative staphylococci (CoNS) have emerged as major pathogens in healthcare-associated facilities, being S. epidermidis, S. haemolyticus and, more recently, S. lugdunensis, the most clinically relevant species. Despite being less virulent than the well-studied pathogen S. aureus, the number of CoNS strains sequenced is constantly increasing and, with that, the number of virulence factors identified in those strains. In this regard, biofilm formation is considered the most important. Besides virulence factors, the presence of several antibiotic-resistance genes identified in CoNS is worrisome and makes treatment very challenging. In this review, we analyzed the different aspects involved in CoNS virulence and their impact on health and food.
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Affiliation(s)
- Angela França
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (V.G.); (N.L.)
| | | | | | - Luís D. R. Melo
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (V.G.); (N.L.)
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Wolden R, Pain M, Karlsson R, Karlsson A, Aarag Fredheim EG, Cavanagh JP. Identification of surface proteins in a clinical Staphylococcus haemolyticus isolate by bacterial surface shaving. BMC Microbiol 2020; 20:80. [PMID: 32264835 PMCID: PMC7137321 DOI: 10.1186/s12866-020-01778-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The skin commensal Staphylococcus haemolyticus is an emerging nosocomial pathogen. Despite its clinical relevance, published information about S. haemolyticus virulence factors is scarce. In this study, the adhesive and biofilm forming properties of ten clinical and ten commensal S. haemolyticus strains were examined using standard adhesion and biofilm assays. One of the clinical strains was used to identify expressed surface proteins using bacterial surface shaving. Protein abundance was examined by a comparative analysis between bacterial protein expression after human keratinocyte (HaCaT) colonization and growth in cell culture media supplemented with serum. Relative protein quantification was performed by labeling peptides with tandem mass tags (TMT) prior to Mass Spectrometry analysis. Surface proteins can be used as novel targets for antimicrobial treatment and in diagnostics. RESULTS Adherence to fibronectin, collagen and plastic was low in all tested strains, but with significantly higher adhesion to fibronectin (p = 0.041) and collagen (p = 0.001) in the commensal strains. There was a trend towards higher degree of biofilm formation in the clinical strains (p = 0.059). By using surface shaving, 325 proteins were detected, of which 65 were classified as surface proteins. Analyses showed that the abundance of nineteen (5.8%) proteins were significantly changed following HaCaT colonization. The bacterial Toll/interleukin-1 like (TIRs) domain containing protein (p = 0.04), the transglycosylase SceD (p = 0.01), and the bifunctional autolysin Atl (p = 0.04) showed a 1.4, 1.6- and 1.5-fold increased abundance. The staphylococcal secretory antigen (SsaA) (p = 0.04) was significantly downregulated (- 1.5 fold change) following HaCaT colonization. Among the 65 surface proteins the elastin binding protein (Ebps), LPXAG and LPXSG domain containing proteins and five LPXTG domain containing proteins were identified; three Sdr-like proteins, the extracellular matrix binding protein Embp and a SasH-like protein. CONCLUSIONS This study has provided novel knowledge about expression of S. haemolyticus surface proteins after direct contact with eukaryotic cells and in media supplemented with serum. We have identified surface proteins and immune evasive proteins previously only functionally described in other staphylococcal species. The identification of expressed proteins after host-microbe interaction offers a tool for the discovery and design of novel targets for antimicrobial treatment.
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Affiliation(s)
- Runa Wolden
- Pediatric Research group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maria Pain
- Pediatric Research group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Roger Karlsson
- Nanoxis Consulting AB, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-413 46, Gothenburg, Region Västra Götaland, Sweden
| | | | - Elizabeth G Aarag Fredheim
- Microbial Pharmacology and Population Biology, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jorunn Pauline Cavanagh
- Pediatric Research group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.
- Department of Pediatrics, The University Hospital of North Norway, Tromsø, Norway.
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13
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The MSCRAMM Family of Cell-Wall-Anchored Surface Proteins of Gram-Positive Cocci. Trends Microbiol 2019; 27:927-941. [PMID: 31375310 DOI: 10.1016/j.tim.2019.06.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/10/2019] [Accepted: 06/19/2019] [Indexed: 01/21/2023]
Abstract
The microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) are a family of proteins that are defined by the presence of two adjacent IgG-like folded subdomains. These promote binding to ligands by mechanisms that involve major conformational changes exemplified by the binding to fibrinogen by the 'dock-lock-latch' mechanism or to collagen by the 'collagen hug'. Clumping factors A and B are two such MSCRAMMs that have several important roles in the pathogenesis of Staphylococcus aureus infections. MSCRAMM architecture, ligand binding, and roles in infection and colonization are examined with a focus on recent developments with clumping factors.
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14
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Abbondio M, Fois I, Longheu C, Azara E, Tola S. Biofilm production, quorum sensing system and analysis of virulence factors of Staphylococcus epidermidis collected from sheep milk samples. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Nagendrababu V, Sheriff Sultan O, Kannathasan S, Patel AS, Chitra E, Neelakantan P, Davamani F. Root canal irrigants influence the hydrophobicity and adherence of Staphylococcus epidermidis to root canal dentin: an in vitro study. Restor Dent Endod 2017; 43:e1. [PMID: 29487832 PMCID: PMC5816986 DOI: 10.5395/rde.2018.43.e1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/06/2017] [Indexed: 12/23/2022] Open
Abstract
Objectives To determine the effect of root canal irrigants on the hydrophobicity and adherence of Staphylococcus epidermidis (S. epidermidis) to root canal dentin in vitro. Materials and Methods Root dentin blocks (n = 60) were randomly divided into 4 groups based on the irrigation regimen: group 1, saline; group 2, 5.25% sodium hypochlorite (NaOCl); group 3, 5.25% NaOCl followed by 17% ethylenediaminetetraacetic acid (EDTA); group 4, same as group 3 followed by 2% chlorhexidine (CHX). The hydrophobicity of S. epidermidis to root dentin was calculated by cell surface hydrophobicity while the adherence was observed by fluorescence microscopy, and bacteria were quantified using ImageJ software (National Institutes of Health). Statistical analysis of the data was done using Kruskal-Wallis test and Mann-Whitney U test (p = 0.05). Results The hydrophobicity and adherence of S. epidermidis to dentin were significantly increased after irrigating with group 3 (NaOCl-EDTA) (p < 0.05), whereas in group 4 (NaOCl-EDTA-CHX) both hydrophobicity and adherence were significantly reduced (p < 0.05). Conclusions The adherence of S. epidermidis to dentin was influenced differently by root canal irrigants. Final irrigation with CHX reduces the bacterial adherence and may impact biofilm formation.
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Affiliation(s)
- Venkateshbabu Nagendrababu
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | - Omer Sheriff Sultan
- Division of Clinical Dentistry, School of Dentistry, International Medical University, Kuala Lumpur, Malaysia
| | | | - Amir Shahreza Patel
- School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Ebenezer Chitra
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
| | - Prasanna Neelakantan
- Discipline of Endodontology, Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | - Fabian Davamani
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
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