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Kellgren T, Dwibedi C, Widerström M, Sundell D, Öhrman C, Sjödin A, Monsen T, Rydén P, Johansson A. Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215. BMC Microbiol 2024; 24:215. [PMID: 38890594 PMCID: PMC11186124 DOI: 10.1186/s12866-024-03367-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings. RESULTS We completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination's role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30-50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2. CONCLUSIONS This study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.
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Affiliation(s)
- Therese Kellgren
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, SE, 90187, Sweden
| | - Chinmay Dwibedi
- Department of Clinical Microbiology and Molecular Infection Medicine Sweden (MIMS), Umeå University, 90185, Umeå, Sweden
| | - Micael Widerström
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden.
| | - David Sundell
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Caroline Öhrman
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Andreas Sjödin
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Tor Monsen
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, SE, 90187, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology and Molecular Infection Medicine Sweden (MIMS), Umeå University, 90185, Umeå, Sweden
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Barrios-Villa E, Mendez-Pfeiffer P, Valencia D, Caporal-Hernandez L, Ballesteros-Monrreal MG. Intracellular bacterial communities in patient with recurrent urinary tract infection caused by Staphylococcus spp and Streptococcus agalactiae: a case report and literature review. AFRICAN JOURNAL OF UROLOGY 2022. [DOI: 10.1186/s12301-022-00314-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Urinary tract infections (UTI) are among the most frequent pathologies worldwide. Uropathogenic Escherichia coli (UPEC) is the leading etiological agent; however, depending on the patient's characteristics, the etiology may include some atypical pathogens. Some pathogenic bacteria can internalize in the urothelial and phagocytic cells complicating treatment and timely diagnosis.
Case presentation
We present a clinical case of a married female patient with urological alteration, constant catheterization, and urethral dilation with recurrent UTI for ten years, with five episodes per year and reports of negative urine culture. The microscopic analysis revealed intracellular bacterial communities (IBC) and pyocytes with active bacteria. A protocol was designed for the release of intracellular bacteria in urine samples; without the proposed treatment, the urine culture was negative. However, upon releasing the internalized bacteria, we obtained a polymicrobial urine culture. We isolated and identified Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus simulans, and Streptococcus agalactiae. All microorganisms were sensitive to nitrofurans and sulfas. The patient is under treatment with nitrofurantoin and continuous follow-up by our workgroup.
Conclusions
It is essential to look for IBC and pyocytes with active bacteria in patients with recurrent UTIs to avoid false-negative urine culture results and provide timely treatment. Polymicrobial culture must be considered depending on the patient and clinical history.
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Martínez-Santos VI, Torres-Añorve DA, Echániz-Aviles G, Parra-Rojas I, Ramírez-Peralta A, Castro-Alarcón N. Characterization of Staphylococcus epidermidis clinical isolates from hospitalized patients with bloodstream infection obtained in two time periods. PeerJ 2022; 10:e14030. [PMID: 36213498 PMCID: PMC9541613 DOI: 10.7717/peerj.14030] [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: 04/11/2022] [Accepted: 08/16/2022] [Indexed: 01/19/2023] Open
Abstract
Background In recent years Staphylococcus epidermidis has been considered an important and frequent causative agent of health care-associated infections (HAIs), increasing the costs of hospitalization, morbidity, and mortality. Antibiotic resistance and biofilm formation are the most important obstacles in the treatment of infections caused by this microorganism. The aim of this work was to determine the most prevalent STs, as well as the antibiotic resistance profile and biofilm formation of S. epidermidis clinical isolates obtained from hospitalized patients in two hospitals in Acapulco, Guerrero in two time periods. Methods Twenty methicillin-resistant S. epidermidis strains isolated from patients with bacteremia in two hospitals in two time periods were analyzed. Identification and antibiotic susceptibility were performed using the Vitek automated system. Molecular confirmation of the identification and methicillin resistance was performed by duplex PCR of the mecA and nuc genes. Biofilm production was analyzed, and the clonal origin was determined by multilocus sequence typing (MLST). Results We identified 14 antibiotic resistance profiles as well as 13 sequence types (ST), including the new ST761. We also found that ST2 and ST23 were the most prevalent and, together with ST59, were found in both time periods. Seventeen of our clinical isolates were multidrug-resistant, but all of them were sensitive to linezolid and vancomycin, and this was not related to biofilm production. Additionally, we standardized a duplex PCR to identify methicillin-resistant S. epidermidis strains. In conclusion, S. epidermidis STs 2, 23, and 59 were found in both time periods. This study is the first report of S. epidermidis ST761. The clinical isolates obtained in this work showed a high multidrug resistance that is apparently not related to biofilm production.
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Affiliation(s)
| | - David A. Torres-Añorve
- Laboratorio de Investigación en Microbiología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Gabriela Echániz-Aviles
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Isela Parra-Rojas
- Labotatorio de Investigación en Obesidad y Diabetes, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Arturo Ramírez-Peralta
- Laboratorio de Investigación en Patometabolismo Microbiano, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Natividad Castro-Alarcón
- Laboratorio de Investigación en Microbiología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
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Jin Y, Wang Q, Zhang H, Zhao N, Yang Z, Wang H, Li M, Liu Q. Phenol-soluble modulin contributes to the dispersal of Staphylococcus epidermidis isolates from catheters. Front Microbiol 2022; 13:934358. [PMID: 35958143 PMCID: PMC9358717 DOI: 10.3389/fmicb.2022.934358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus epidermidis (S. epidermidis), a human commensal, has been implicated in invasive infection in humans due to their ability to form biofilm. It is assumed that when a biofilm is dispersed it will subsequently cause a more severe infection. The clinical significance of S. epidermidis isolated from sterile body fluid (BF) remains unclear, and might be related to dispersal from catheter-associated biofilm infection. To evaluate this relationship, we evaluated S. epidermidis isolates from catheters (CA) or BF in hospitalized patients. Sequence type 2 (ST2) is the most prevalent type isolated from infection sites. Although the specific STs were also observed in isolates from different sites, we observed that the main sequence type was ST2, followed by ST59, among all the 114 isolates from different infection sites. Interestingly, ST2 strains isolated from BF exhibited significantly thicker biofilm than those from CA. The thicker biofilm was due to the higher expression of accumulation-associated protein (aap) but not intercellular adhesion (ica) operon. Moreover, the transcription of PSMδ and PSMε were significantly increased in ST2 strains isolated from BF. Although the bacterial loads on catheters were similar infected by CA- or BF-originated strains in mouse biofilm-associated infection model, we observed a higher CFU in peri-catheter tissues infected by ST2 clones isolated from BF, suggesting that S. epidermidis with thicker biofilm formation might be able to disperse. Taken together, our data suggested that S. epidermidis originated from diverse infection sites exhibited different biofilm forming capacity. The major ST2 clone isolated from BF exhibited thicker biofilm by increasing the expression of Aap. The higher expression of PSM of these strains may contribute to bacteria dispersal from biofilm and the following bacterial spread.
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Mirzaei R, Alikhani MY, Arciola CR, Sedighi I, Yousefimashouf R, Bagheri KP. Prevention, inhibition, and degradation effects of melittin alone and in combination with vancomycin and rifampin against strong biofilm producer strains of methicillin-resistant Staphylococcus epidermidis. Biomed Pharmacother 2022; 147:112670. [PMID: 35123230 DOI: 10.1016/j.biopha.2022.112670] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus epidermidis (MRSE) bacteria are being recognized as true pathogens as they are able to resist methicillin and commonly form biofilms. Recent studies have shown that antimicrobial peptides (AMPs) are promising agents against biofilm-associated bacterial infections. In this study, we aimed to explore the antibiofilm activity of melittin, either alone or in combination with vancomycin and rifampin, against biofilm-producing MRSE strains. Minimum biofilm preventive concentration (MBPC), minimum biofilm inhibition concentration (MBIC), and minimum biofilm eradication concentration (MBEC), as well as fractional biofilm preventive-, inhibitory-, and eradication concentrations (FBPCi, FBICi, and FBECi), were determined for the antimicrobial agents tested. Cytotoxicity and hemolytic activity of melittin at its synergistic concentration were examined on human embryonic kidney cells (HEK-293) and Red Blood Cells (RBCs), respectively. The effect of melittin on the downregulation of biofilm-associated genes was explored using Real-Time PCR. MBPC, MBIC, and MBEC values for melittin were in the range of 0.625-20, 0.625-20, and 10-40 μg/μL, respectively. Melittin showed high synergy (FBPCi, FBICi and FBECi < 0.5). The synergism resulted in a 64-512-fold, 2-16 and 2-8-fold reduction in melittin, rifampicin and vancomycin concentrations, respectively. The synergistic melittin concentration found to be effective did not manifest either cytotoxicity on HEK-293 or hemolytic activity on RBCs. Results showed that melittin downregulated the expression of biofilm-associated icaA, aap, and psm genes in all isolates tested, ranging from 0.04-folds to 2.11-folds for icaA and from 0.05 to 3.76-folds for aap and psm. The preventive and therapeutic indexes of melittin were improved 8-fold when combined with vancomycin and rifampin. Based on these findings, the combination of melittin with conventional antibiotics could be proposed for treating or preventing biofilm-associated MRSE infections.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Yousef Alikhani
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Carla Renata Arciola
- Laboratorio di Patologia delle Infezioni Associate all'Impianto IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy; Laboratorio di Immunoreumatologia e Rigenerazione Tissutale, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy; Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Iraj Sedighi
- Department of Pediatrics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rasoul Yousefimashouf
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Kamran Pooshang Bagheri
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Viability-Resolved Metagenomics Reveals Antagonistic Colonization Dynamics of Staphylococcus epidermidis Strains on Preterm Infant Skin. mSphere 2021; 6:e0053821. [PMID: 34523979 PMCID: PMC8550141 DOI: 10.1128/msphere.00538-21] [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] [Indexed: 11/23/2022] Open
Abstract
Preterm infants are at increased risk of infections caused by coagulase-negative staphylococci (CoNS) that colonize skin. Technical barriers in sequencing low-microbial-biomass skin swabs from preterm infants hinder attempts to gain a strain-level understanding of CoNS colonization dynamics within their developing skin microbiome. Here, the microbiome of five skin sites and available stool was studied from four preterm infants hospitalized over their first 2 months of life. We used propidium monoazide treatment of samples to enrich for the viable microbiome and metagenomic shotgun sequencing to resolve species and strains. The microbiome of different skin sites overlapped with each other, was dominated by the CoNS species Staphylococcus epidermidis and Staphylococcus capitis, and was distinct from stool. Species diversity on skin increased over time despite antibiotic exposure. Evidence of antagonism between the most common S. epidermidis strains, ST2 and ST59, included negative relationships for species correlation networks and in situ replication rates and that ST2 colonized skin earlier but was often replaced by ST59 over time. Experiments done with reference isolates showed that ST2 produced more biofilm than ST59 on plastic surfaces, which was reduced in mixed culture. We also discovered that a rare S. epidermidis strain, ST5, grew rapidly in stool in association with Stenotrophomonas maltophilia from a suspected episode of infection. Viability treatment of samples and moderate throughput shotgun sequencing provides strain-level information about CoNS colonization dynamics of preterm infant skin that ultimately might be exploited to prevent infections. IMPORTANCE The skin is a habitat for microbes that commonly infect preterm infants, but the use of sequencing for fine-scale study of the microbial communities of skin that develop in these infants has been limited by technical barriers. We treated skin swabs of preterm infants with a photoreactive dye that eliminates DNA from nonviable microbes and then sequenced the remaining DNA. We found that two strains of the most common species, Staphylococcus epidermidis, showed an antagonistic relationship on skin by cooccurring with different species, replicating fastest in different samples, and dominating skin sites at different times. Representatives of these strains also differed in their ability to stick to plastic surfaces—an important pathogenicity trait of this species. Our study shows the feasibility of gaining detailed information about strain colonization dynamics from this difficult-to-sequence body site of preterm infants, which might be used to guide novel approaches to prevent infections.
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Widerström M, Stegger M, Johansson A, Gurram BK, Larsen AR, Wallinder L, Edebro H, Monsen T. Heterogeneity of Staphylococcus epidermidis in prosthetic joint infections: time to reevaluate microbiological criteria? Eur J Clin Microbiol Infect Dis 2021; 41:87-97. [PMID: 34599708 PMCID: PMC8732909 DOI: 10.1007/s10096-021-04352-w] [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: 06/08/2021] [Accepted: 09/17/2021] [Indexed: 11/24/2022]
Abstract
Prosthetic joint infection (PJI) is a feared and challenging to diagnose complication after arthroplasty, with Staphylococcus epidermidis as the major pathogen. One important criteria to define PJI is the detection of phenotypically indistinguishable microorganisms with identical antibiotic susceptibility pattern in at least two different samples. However, owing to phenotypical variation within genetic clones and clonal variation within a phenotype, the criteria may be ambiguous. We investigated the extent of diversity among coagulase-negative staphylococci (CoNS) in PJI and characterised S. epidermidis isolates from PJI samples, specifically multiple S. epidermidis isolates identified in individual PJI patients. We performed a retrospective cohort study on 62 consecutive patients with PJI caused by CoNS from two hospitals in Northern Sweden. In 16/62 (26%) PJIs, multiple S. epidermidis isolates were available for whole-genome analyses. Hospital-adapted multidrug-resistant genetic clones of S. epidermidis were identified in samples from 40/62 (65%) of the patients using a combination of pulsed-field gel electrophoresis and multilocus sequence typing. Whole-genome sequencing showed the presence of multiple sequence types (STs) in 7/16 (44%) PJIs where multiple S. epidermidis isolates were available. Within-patient phenotypical variation in the antibiotic susceptibility and/or whole-genome antibiotic resistance gene content was frequent (11/16, 69%) among isolates with the same ST. The results highlight the ambiguity of S. epidermidis phenotypic characterisation as a diagnostic method in PJI and call for larger systematic studies for determining the frequency of CoNS diversity in PJIs, the implications of such diversity for microbiological diagnostics, and the therapeutic outcomes in patients.
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Affiliation(s)
- Micael Widerström
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden.
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Bharat Kumar Gurram
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Wallinder
- Department of Orthopaedics, University Hospital of Umeå, Umeå, Sweden
| | - Helen Edebro
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Tor Monsen
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
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Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle. Nat Microbiol 2021; 6:757-768. [PMID: 34031577 DOI: 10.1038/s41564-021-00913-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Most clonal lineages of Staphylococcus epidermidis are commensals present on human skin and in the nose. However, some globally spreading healthcare-associated and methicillin-resistant S. epidermidis (HA-MRSE) clones are major causes of difficult-to-treat implant or bloodstream infections. The molecular determinants that alter the lifestyle of S. epidermidis have remained elusive, and their identification might provide therapeutic targets. We reasoned that changes in surface-exposed wall teichoic acid (WTA) polymers of S. epidermidis, which potentially shape host interactions, may be linked to differences between colonization and infection abilities of different clones. We used a combined epidemiological and functional approach to show that while commensal clones express poly-glycerolphosphate WTA, S. epidermidis multilocus sequence type 23, which emerged in the past 15 years and is one of the main infection-causing HA-MRSE clones, contains an accessory genetic element, tarIJLM, that leads to the production of a second, Staphylococcus aureus-type WTA (poly-ribitolphosphate (RboP)). Production of RboP-WTA by S. epidermidis impaired in vivo colonization but augmented endothelial attachment and host mortality in a mouse sepsis model. tarIJLM was absent from commensal human sequence types but was found in several other HA-MRSE clones. Moreover, RboP-WTA enabled S. epidermidis to exchange DNA with S. aureus via siphovirus bacteriophages, thereby creating a possible route for the inter-species exchange of methicillin resistance, virulence and colonization factors. We conclude that tarIJLM alters the lifestyle of S. epidermidis from commensal to pathogenic and propose that RboP-WTA might be a robust target for preventive and therapeutic interventions against MRSE infections.
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Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations. PLoS Pathog 2021; 17:e1009304. [PMID: 33544760 PMCID: PMC7891712 DOI: 10.1371/journal.ppat.1009304] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/18/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
S. epidermidis is a substantial component of the human skin microbiota, but also one of the major causes of nosocomial infection in the context of implanted medical devices. We here aimed to advance the understanding of S. epidermidis genotypes and phenotypes conducive to infection establishment. Furthermore, we investigate the adaptation of individual clonal lines to the infection lifestyle based on the detailed analysis of individual S. epidermidis populations of 23 patients suffering from prosthetic joint infection. Analysis of invasive and colonizing S. epidermidis provided evidence that invasive S. epidermidis are characterized by infection-supporting phenotypes (e.g. increased biofilm formation, growth in nutrient poor media and antibiotic resistance), as well as specific genetic traits. The discriminating gene loci were almost exclusively assigned to the mobilome. Here, in addition to IS256 and SCCmec, chromosomally integrated phages was identified for the first time. These phenotypic and genotypic features were more likely present in isolates belonging to sequence type (ST) 2. By comparing seven patient-matched nasal and invasive S. epidermidis isolates belonging to identical genetic lineages, infection-associated phenotypic and genotypic changes were documented. Besides increased biofilm production, the invasive isolates were characterized by better growth in nutrient-poor media and reduced hemolysis. By examining several colonies grown in parallel from each infection, evidence for genetic within-host population heterogeneity was obtained. Importantly, subpopulations carrying IS insertions in agrC, mutations in the acetate kinase (AckA) and deletions in the SCCmec element emerged in several infections. In summary, these results shed light on the multifactorial processes of infection adaptation and demonstrate how S. epidermidis is able to flexibly repurpose and edit factors important for colonization to facilitate survival in hostile infection environments. S. epidermidis is a substantial component of the human skin microbiota, but also a major cause of nosocomial infections related to implanted medical devices. While phenotypic and genotypic determinants supporting invasion were identified, none appears to be necessary. By analysis of S. epidermidis from prosthetic joint infections, we here show that adaptive events are of importance during the transition from commensalism to infection. Adaptation to the infectious lifestyle is characterised by the development of intra-clonal heterogeneity, increased biofilm formation and enhanced growth in iron-free and nutrient-poor media, as well as reduced production of hemolysins. Importantly, during infection subpopulations emerge that carry mutations in a number of genes, most importantly the acetate kinase (ackA) and the β-subunit of the RNA polymerase (rpoB), have deleted larger chromosomal fragments (e.g. within the SCCmec element) or IS insertions in AgrC, a component of the master quorum sensing system in S. epidermidis. These results shed light on the multifactorial processes of infection adaptation and demonstrate how S. epidermidis is able to flexibly repurpose and edit factors important for colonization to facilitate survival under hostile infection conditions. While mobilome associated factors are important for S. epidermidis invasive potential, the species possesses a multi-layered and complex ability for adaptation to hostile environments, supporting the progression to chronic implant-associated infections.
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Palusińska-Szysz M, Zdybicka-Barabas A, Frąc M, Gruszecki WI, Wdowiak-Wróbel S, Reszczyńska E, Skorupska D, Mak P, Cytryńska M. Identification and characterization of Staphylococcus spp. and their susceptibility to insect apolipophorin III. Future Microbiol 2020; 15:1015-1032. [PMID: 32811181 DOI: 10.2217/fmb-2019-0328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study investigated the effect of an insect antimicrobial protein, apolipophorin III (apoLp-III), against two newly isolated, identified and characterized clinical strains of Staphylococcus spp. Materials & methods: Both strains were identified by 16S rRNA sequencing and metabolic and phenotypic profiling. The antibacterial activity of apoLp-III was tested using a colony counting assay. ApoLp-III interaction with bacterial cell surface was analyzed by Fourier transform IR spectroscopy. Results: Staphylococcus epidermidis and Staphylococcus capitis were identified. ApoLp-III exerted a dose-dependent bactericidal effect on the tested strains. The differences in the Staphylococcus spp. surface components may contribute to the various sensitivities of these strains to apoLp-III. Conclusion: ApoLp-III may provide a baseline for development of antibacterial preparations against Staphylococcus spp. involved in dermatological problems.
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Affiliation(s)
- Marta Palusińska-Szysz
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology & Biotechnology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Agnieszka Zdybicka-Barabas
- Department of Immunobiology, Institute of Biological Sciences, Faculty of Biology & Biotechnology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4 St., 20-290 Lublin, Poland
| | - Wiesław I Gruszecki
- Department of Biophysics, Institute of Physics, Maria Curie-Skłodowska University, Maria Curie-Skłodowska Square 1, 20-031 Lublin, Poland
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology & Biotechnology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Emilia Reszczyńska
- Department of Plant Physiology & Biophysics, Institute of Biological Sciences, Faculty of Biology & Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | | | - Paweł Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics & Biotechnology, Jagiellonian University, Gronostajowa 7 St., 30-387 Krakow
| | - Małgorzata Cytryńska
- Department of Immunobiology, Institute of Biological Sciences, Faculty of Biology & Biotechnology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
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Arora S, Li X, Hillhouse A, Konganti K, Little SV, Lawhon SD, Threadgill D, Shelburne S, Hook M. Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands. mBio 2020; 11:e02911-19. [PMID: 32071265 PMCID: PMC7029136 DOI: 10.1128/mbio.02911-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/08/2020] [Indexed: 01/18/2023] Open
Abstract
Staphylococcus epidermidis is a leading cause of nosocomial infections in patients with a compromised immune system and/or an implanted medical device. Seventy to 90% of S. epidermidis clinical isolates are methicillin resistant and carry the mecA gene, present in a mobile genetic element (MGE) called the staphylococcal cassette chromosome mec (SCCmec) element. Along with the presence of antibiotic and heavy metal resistance genes, MGEs can also contain genes encoding secreted or cell wall-anchored virulence factors. In our earlier studies of S. epidermidis clinical isolates, we discovered S. epidermidis surface protein J (SesJ), a prototype of a recently discovered subfamily of the microbial surface component recognizing adhesive matrix molecule (MSCRAMM) group. MSCRAMMs are major virulence factors of pathogenic Gram-positive bacteria. Here, we report that the sesJ gene is always accompanied by two glycosyltransferase genes, gtfA and gtfB, and is present in two MGEs, called the arginine catabolic mobile element (ACME) and the staphylococcal cassette chromosome (SCC) element. The presence of the sesJ gene was associated with the left-hand direct repeat DR_B or DR_E. When inserted via DR_E, the sesJ gene was encoded in the SCC element. When inserted via DR_B, the sesJ gene was accompanied by the genes for the type 1 restriction modification system and was encoded in the ACME. Additionally, the SCC element and ACME carry different isoforms of the SesJ protein. To date, the genes encoding MSCRAMMs have been seen to be located in the bacterial core genome. Here, we report the presence of an MSCRAMM in an MGE in S. epidermidis clinical isolates.IMPORTANCES. epidermidis is an opportunistic bacterium that has established itself as a successful nosocomial pathogen. The modern era of novel therapeutics and medical devices has extended the longevity of human life, but at the same time, we also witness the evolution of pathogens to adapt to newly available niches in the host. Increasing antibiotic resistance among pathogens provides an example of such pathogen adaptation. With limited opportunities to modify the core genome, most of the adaptation occurs by acquiring new genes, such as virulence factors and antibiotic resistance determinants present in MGEs. In this study, we describe that the sesJ gene, encoding a recently discovered cell wall-anchored protein in S. epidermidis, is present in both ACME and the SCC element. The presence of virulence factors in MGEs can influence the virulence potential of a specific strain. Therefore, it is critical to study the virulence factors found in MGEs in emerging pathogenic bacteria or strains to understand the mechanisms used by these bacteria to cause infections.
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Affiliation(s)
- Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas, USA
| | - Xiqi Li
- Department of Infectious Diseases, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Andrew Hillhouse
- Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas, USA
| | - Kranti Konganti
- Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas, USA
| | - Sara V Little
- Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Sara D Lawhon
- Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - David Threadgill
- Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas, USA
| | - Samuel Shelburne
- Department of Infectious Diseases, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas, USA
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12
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Cabrera-Contreras R, Santamaría RI, Bustos P, Martínez-Flores I, Meléndez-Herrada E, Morelos-Ramírez R, Barbosa-Amezcua M, González-Covarrubias V, Silva-Herzog E, Soberón X, González V. Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children's Hospital in México City in an eight-years survey. PeerJ 2019; 7:e8068. [PMID: 31768302 PMCID: PMC6874853 DOI: 10.7717/peerj.8068] [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: 04/29/2019] [Accepted: 10/20/2019] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children's health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.
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Affiliation(s)
- Roberto Cabrera-Contreras
- Laboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Irma Martínez-Flores
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Meléndez-Herrada
- Laboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rubén Morelos-Ramírez
- Laboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | | | | | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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13
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Cave R, Misra R, Chen J, Wang S, Mkrtchyan HV. Whole genome sequencing revealed new molecular characteristics in multidrug resistant staphylococci recovered from high frequency touched surfaces in London. Sci Rep 2019; 9:9637. [PMID: 31371820 PMCID: PMC6675788 DOI: 10.1038/s41598-019-45886-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/13/2019] [Indexed: 01/15/2023] Open
Abstract
The rise of antibiotic resistance (AMR) is one of the most important public health threats worldwide.Today, increasing attention is being paid to multidrug resistant staphylococci isolated from healthcare and non-healthcare environments as the treatment of these bacteria has become increasingly difficult. In this study, we compared staphylococci isolates recovered from high frequency touched surfaces from public areas in the community and hospitals in East and West London. 281 out of 600 (46.83%) staphylococci isolates recovered were multidrug resistant, of which 49 (8.17%) were mecA positive. There was significantly higher proportion of multidrug resistant staphylococci (P = 0.0002) in East London (56.7%) compared to West London (49.96%). The most common species identified as multidrug resistant were S. epidermidis, S. haemolyticus and S. hominis, whereas penicillin, fusidic acid and erythromycin were the most frequent antibiotics the isolates were resistant to. Whole genome sequenced of mecA positive isolates revealed that S. sciuri isolates carried the mecA1 gene, which has only 84.43% homology with mecA. In addition, other frequently identified resistance genes included blaZ, qacA/B and dfrC. We have also identified a diverse range of SCCmec types, many of which were untypable due to carrying a novel combination of ccr genes or multiple ccr complexes.
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Affiliation(s)
- Rory Cave
- University of East London, School of Health, Sport and Bioscience, Water Lane, London, E15 4LZ, UK
| | - Raju Misra
- Natural History Museum, Core Research Laboratories, Molecular Biology, Cromwell Rd, London, SW7 5BD, UK
| | - Jiazhen Chen
- Department of Infectious Disease, Huashan Hospital, Fudan University, 12 Middle Wulumuqi Rd., Shanghai, 200040, China
| | - Shiyong Wang
- Department of Infectious Disease, Huashan Hospital, Fudan University, 12 Middle Wulumuqi Rd., Shanghai, 200040, China
| | - Hermine V Mkrtchyan
- University of East London, School of Health, Sport and Bioscience, Water Lane, London, E15 4LZ, UK.
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A Novel, Widespread qacA Allele Results in Reduced Chlorhexidine Susceptibility in Staphylococcus epidermidis. Antimicrob Agents Chemother 2019; 63:AAC.02607-18. [PMID: 30988144 DOI: 10.1128/aac.02607-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/13/2019] [Indexed: 12/12/2022] Open
Abstract
Chlorhexidine gluconate (CHG) is a topical antiseptic widely used in health care settings. In Staphylococcus spp., the pump QacA effluxes CHG, while the closely related QacB cannot due to a single amino acid substitution. We characterized 1,050 cutaneous Staphylococcus isolates obtained from 173 pediatric oncology patients enrolled in a multicenter CHG bathing trial. CHG susceptibility testing revealed that 63 (6%) of these isolates had elevated CHG MICs (≥4 μg/ml). Screening of all 1,050 isolates for the qacA/B gene (the same qac gene with A or B allele) by restriction fragment length polymorphism (RFLP) yielded 56 isolates with a novel qacA/B RFLP pattern, qacA/B273 The CHG MIC was significantly higher for qacA/B273 -positive isolates (MIC50, 4 μg/ml; MIC range, 0.5 to 4 μg/ml) than for other qac groups: qacA-positive isolates (n = 559; MIC50, 1 μg/ml; MIC range, 0.5 to 4 μg/ml), qacB-positive isolates (n = 17; MIC50, 1 μg/ml; MIC range, 0.25 to 2 μg/ml), and qacA/B-negative isolates (n = 418, MIC50, 1 μg/ml; MIC range, 0.125 to 2 μg/ml) (P = 0.001). A high proportion of the qacA/B273 -positive isolates also displayed methicillin resistance (96.4%) compared to the other qac groups (24.9 to 61.7%) (P = 0.001). Whole-genome sequencing revealed that qacA/B273 -positive isolates encoded a variant of QacA with 2 amino acid substitutions. This new allele, named qacA4, was carried on the novel plasmid pAQZ1. The qacA4-carrying isolates belonged to the highly resistant Staphylococcus epidermidis sequence type 2 clone. By searching available sequence data sets, we identified 39 additional qacA4-carrying S. epidermidis strains from 5 countries. Curing an isolate of qacA4 resulted in a 4-fold decrease in the CHG MIC, confirming the role of qacA4 in the elevated CHG MIC. Our results highlight the importance of further studying qacA4 and its functional role in clinical staphylococci.
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15
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Heilmann C, Ziebuhr W, Becker K. Are coagulase-negative staphylococci virulent? Clin Microbiol Infect 2018; 25:1071-1080. [PMID: 30502487 DOI: 10.1016/j.cmi.2018.11.012] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/06/2018] [Accepted: 11/11/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Progress in contemporary medicine is associated with an increasing number of immunocompromised individuals. In this vulnerable group, the underlying disease together with long-term hospitalization and the use of medical devices facilitate infections by opportunistic pathogens, of which coagulase-negative staphylococci (CoNS) represent a prime example. OBJECTIVES The diversity of CoNS with species- and strain-specific differences concerning virulence and clinical impact is highlighted. A focus is on the ability of CoNS to generate biofilms on biotic and abiotic surfaces, which enables skin and mucosa colonization as well as establishment of CoNS on indwelling foreign bodies. SOURCES Literature about the virulence of CoNS listed in PubMed was reviewed. CONTENT Most catheter-related and prosthetic joint infections as well as most other device-related infections are caused by CoNS, specifically by Staphylococcus epidermidis and Staphylococcus haemolyticus. A common theme of CoNS infections is a high antibiotic resistance rate, which often limits treatment options and contributes to the significant health and economic burden imposed by CoNS. IMPLICATIONS Breaching the skin barrier along with the insertion of medical devices offers CoNS opportunities to gain access to host tissues and to sustain there by forming biofilms on foreign body surfaces. Biofilms represent the perfect niche to protect CoNS from both the host immune response and the action of antibiotics. Their particular lifestyle, combined with conditions that facilitate host colonization and infection, has led to the growing impact of CoNS as pathogens. Moreover, CoNS may serve as hidden reservoirs for antibiotic resistance and virulence traits.
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Affiliation(s)
- C Heilmann
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - W Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - K Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
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16
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Månsson E, Söderquist B, Nilsdotter-Augustinsson Å, Särndahl E, Demirel I. Staphylococcus epidermidis from prosthetic joint infections induces lower IL-1β release from human neutrophils than isolates from normal flora. APMIS 2018; 126:678-684. [PMID: 30168623 DOI: 10.1111/apm.12861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/22/2018] [Indexed: 11/27/2022]
Abstract
The aim of this study was to test the hypothesis that Staphylococcus epidermidis isolated from prosthetic joint infections (PJIs) differs from S. epidermidis isolated from normal flora in terms of its capacity to induce activation of caspase-1 and release of IL-1β in human neutrophils. The amount of active caspase-1 was determined over 6 h by detecting Ac-YVAD-AMC fluorescence in human neutrophils incubated with S. epidermidis isolates from PJIs (ST2) or normal flora. The amount of IL-1β was detected by ELISA in neutrophil supernatants after 6 h of incubation. Mean IL-1β release was lower after incubation with S. epidermidis from PJIs compared to isolates from normal flora, but no statistically significant difference was found in active caspase-1. Substantial inter-individual differences in both active caspase-1 and IL-1β were noted. These results suggest that evasion of innate immune response, measured as reduced capacity to induce release of IL-1β from human neutrophils, might be involved in the predominance of ST2 in S. epidermidis PJIs, but that other microbe-related factors are probably also important.
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Affiliation(s)
- Emeli Månsson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Region Västmanland - Uppsala University, Centre for Clinical Research, Hospital of Västmanland, Västerås, Sweden
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Department of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Norrköping, Sweden
| | - Eva Särndahl
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Isak Demirel
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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17
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Sharma S, Chaudhry V, Kumar S, Patil PB. Phylogenomic Based Comparative Studies on Indian and American Commensal Staphylococcus epidermidis Isolates. Front Microbiol 2018. [PMID: 29535698 PMCID: PMC5835047 DOI: 10.3389/fmicb.2018.00333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus epidermidis is a prominent commensal member of human skin microbiome and an emerging nosocomial pathogen, making it a good model organism to provide genomic insights, correlating its transition between commensalism and pathogenicity. While there are numerous studies to understand differences in commensal and pathogenic isolates, systematic efforts to understand variation and evolutionary pattern in multiple strains isolated from healthy individuals are lacking. In the present study, using whole genome sequencing and analysis, we report presence of diverse lineages of S. epidermidis isolates in healthy individuals from two geographically diverse locations of India and North America. Further, there is distinct pattern in the distribution of candidate gene(s) for pathogenicity and commensalism. The pattern is not only reflected in lineages but is also based on geographic origin of the isolates. This is evident by the fact that North American isolates under this study are more genomically dynamic and harbor pathogenicity markers in higher frequency. On the other hand, isolates of Indian origin are less genomically dynamic, harbor less pathogenicity marker genes and possess two unique antimicrobial peptide gene clusters. This study provides a basis to understand the nature of selection pressure in a key human skin commensal bacterium with implications in its management as an opportunistic pathogen.
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Affiliation(s)
- Shikha Sharma
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Vasvi Chaudhry
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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18
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Liu C, Zhang F, Chen C, Feng X, Xu M, Guo X, Sun J, Li G, Zhu P, Zeng L, Xu H, Wang H, Li X, Ming L. Characterization of Teicoplanin NonsusceptibleStaphylococcus epidermidisClinical Isolates Belonging Predominantly to ST267. Microb Drug Resist 2017; 23:321-327. [PMID: 27314582 DOI: 10.1089/mdr.2015.0321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cailin Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Fushan Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Chunguang Chen
- Department of Clinical Laboratory, The Sixth People's Hospital of Zhengzhou City, Zhengzhou, People's Republic of China
| | - Xianju Feng
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
| | - Min Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Xiaobing Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Jingjing Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Guanli Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Pengfei Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Li Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
| | - Hui Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Hongmei Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Xiaogai Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
- Key Clinical Laboratory of Henan Province, Zhengzhou, People's Republic of China
- Department of Laboratory Medicine, Zhengzhou University, Zhengzhou, People's Republic of China
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19
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Colonization of patients, healthcare workers, and the environment with healthcare-associated Staphylococcus epidermidis genotypes in an intensive care unit: a prospective observational cohort study. BMC Infect Dis 2016; 16:743. [PMID: 27938344 PMCID: PMC5148920 DOI: 10.1186/s12879-016-2094-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 12/06/2016] [Indexed: 01/22/2023] Open
Abstract
Background During the last decades, healthcare-associated genotypes of methicillin-resistant Staphylococcus epidermidis (HA-MRSE) have been established as important opportunistic pathogens. However, data on potential reservoirs on HA-MRSE is limited. The aim of the present study was to investigate the dynamics and to which extent HA-MRSE genotypes colonize patients, healthcare workers (HCWs) and the environment in an intensive care unit (ICU). Methods Over 12 months in 2006–2007, swab samples were obtained from patients admitted directly from the community to the ICU and patients transferred from a referral hospital, as well as from HCWs, and the ICU environment. Patients were sampled every third day during hospitalization. Antibiotic susceptibility testing was performed according to EUCAST guidelines. Pulsed-field gel electrophoresis and multilocus sequence typing were used to determine the genetic relatedness of a subset of MRSE isolates. Results We identified 620 MRSE isolates from 570 cultures obtained from 37 HCWs, 14 patients, and 14 environmental surfaces in the ICU. HA-MRSE genotypes were identified at admission in only one of the nine patients admitted directly from the community, of which the majority subsequently were colonized by HA-MRSE genotypes within 3 days during hospitalization. Almost all (89%) of HCWs were nasal carriers of HA-MRSE genotypes. Similarly, a significant proportion of patients transferred from the referral hospital and fomites in the ICU were widely colonized with HA-MRSE genotypes. Conclusions Patients transferred from a referral hospital, HCWs, and the hospital environment serve as important reservoirs for HA-MRSE. These observations highlight the need for implementation of effective infection prevention and control measures aiming at reducing HA-MRSE transmission in the healthcare setting. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2094-x) contains supplementary material, which is available to authorized users.
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20
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Saffari F, Widerström M, Gurram BK, Edebro H, Hojabri Z, Monsen T. Molecular and Phenotypic Characterization of Multidrug-Resistant Clones ofStaphylococcus epidermidisin Iranian Hospitals: Clonal Relatedness to Healthcare-Associated Methicillin-Resistant Isolates in Northern Europe. Microb Drug Resist 2016; 22:570-577. [DOI: 10.1089/mdr.2015.0283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fereshteh Saffari
- Department of Microbiology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Micael Widerström
- Department of Clinical Microbiology, Unit of Research, Education and Development-Östersund, Umeå University, Umeå, Sweden
| | | | - Helen Edebro
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Zoya Hojabri
- Department of Microbiology, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Tor Monsen
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
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21
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Molecular Epidemiology of a Vancomycin-Intermediate Heteroresistant Staphylococcus epidermidis Outbreak in a Neonatal Intensive Care Unit. Antimicrob Agents Chemother 2016; 60:5673-81. [PMID: 27401579 DOI: 10.1128/aac.00726-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/06/2016] [Indexed: 01/05/2023] Open
Abstract
Coagulase-negative staphylococci (CoNS) have become the leading cause of bloodstream infections (BSIs) in intensive care units (ICUs), particularly in premature neonates. Vancomycin-intermediate heteroresistant CoNS (hVICoNS) have been identified as sources of BSIs worldwide, and their potential to emerge as significant pathogens in the neonatal ICU (NICU) remains uncertain. This study describes the molecular epidemiology of an outbreak of vancomycin-heteroresistant (hV) Staphylococcus epidermidis central-line-associated BSI (CLABSI) in a single tertiary care NICU and compares it to a second tertiary care NICU that had not been associated with an outbreak. Between November 2009 and April 2014, 119 S. epidermidis CLABSIs were identified in two tertiary care NICUs in Quebec, Canada. Decreased vancomycin susceptibility was identified in about 88% of all collected strains using Etest methods. However, discrepancies were found according to the Etest and population analysis profiling-area under the concentration-time curve (PAP-AUC) methods used. All strains were susceptible to linezolid, and a few isolates were nonsusceptible to daptomycin. Great genetic diversity was observed within the collection, with 31 pulsed-field gel electrophoresis (PFGE) patterns identified. The outbreak strains were all determined to be heteroresistant to vancomycin and were polyclonal. The study identified two major clones, PFGE patterns E and G, which were found in both NICUs across the 5-year study period. This suggests the persistence of highly successful clones that are well adapted to the hospital environment. hV S. epidermidis seems more common than currently realized in the NICU, and certain hV S. epidermidis clones can become endemic to the NICU. The reservoirs for these clones remain unknown at this time, and identification of the reservoirs is needed to better understand the impact of hV S. epidermidis in the NICU and to inform infection prevention strategies. In addition, there is a need to investigate and validate hV determination protocols for different species of CoNS.
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Lee JYH, Monk IR, Pidot SJ, Singh S, Chua KYL, Seemann T, Stinear TP, Howden BP. Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis. Microb Genom 2016; 2:e000077. [PMID: 28785416 PMCID: PMC5537629 DOI: 10.1099/mgen.0.000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/05/2016] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage is frequently multidrug-resistant and accounts for most of the clinical disease worldwide. However, there are no publically available, closed ST2 genomes and pathogenesis studies have not focused on these strains. We report the complete genome and methylome of BPH0662, a multidrug-resistant, hospital-adapted, ST2 S. epidermidis, and describe the correlation between resistome and phenotype, as well as demonstrate its relationship to publically available, international ST2 isolates. Furthermore, we delineate the methylome determined by the two type I restriction modification systems present in BPH0662 through heterologous expression in Escherichia coli, allowing the assignment of each system to its corresponding target recognition motif. As the first, to our knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable reference for future genomic studies of this clinically relevant lineage. Defining the methylome and the construction of these E. coli hosts provides the foundation for the development of molecular tools to bypass restriction modification systems in this lineage that has hitherto proven intractable.
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Affiliation(s)
- Jean Y. H. Lee
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Ian R. Monk
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | | | - Kyra Y. L. Chua
- Microbiology Department, Austin Health, Melbourne, Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Victorian Life Sciences Computation Inititative, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Benjamin P. Howden
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Infectious Diseases Department, Austin Health, Melbourne, Australia
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Susceptibility to chlorhexidine amongst multidrug-resistant clinical isolates of Staphylococcus epidermidis from bloodstream infections. Int J Antimicrob Agents 2016; 48:86-90. [DOI: 10.1016/j.ijantimicag.2016.04.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/06/2016] [Accepted: 04/16/2016] [Indexed: 11/18/2022]
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Tolo I, Thomas JC, Fischer RSB, Brown EL, Gray BM, Robinson DA. Do Staphylococcus epidermidis Genetic Clusters Predict Isolation Sources? J Clin Microbiol 2016; 54:1711-1719. [PMID: 27076664 PMCID: PMC4922092 DOI: 10.1128/jcm.03345-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/07/2016] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus epidermidis is a ubiquitous colonizer of human skin and a common cause of medical device-associated infections. The extent to which the population genetic structure of S. epidermidis distinguishes commensal from pathogenic isolates is unclear. Previously, Bayesian clustering of 437 multilocus sequence types (STs) in the international database revealed a population structure of six genetic clusters (GCs) that may reflect the species' ecology. Here, we first verified the presence of six GCs, including two (GC3 and GC5) with significant admixture, in an updated database of 578 STs. Next, a single nucleotide polymorphism (SNP) assay was developed that accurately assigned 545 (94%) of 578 STs to GCs. Finally, the hypothesis that GCs could distinguish isolation sources was tested by SNP typing and GC assignment of 154 isolates from hospital patients with bacteremia and those with blood culture contaminants and from nonhospital carriage. GC5 was isolated almost exclusively from hospital sources. GC1 and GC6 were isolated from all sources but were overrepresented in isolates from nonhospital and infection sources, respectively. GC2, GC3, and GC4 were relatively rare in this collection. No association was detected between fdh-positive isolates (GC2 and GC4) and nonhospital sources. Using a machine learning algorithm, GCs predicted hospital and nonhospital sources with 80% accuracy and predicted infection and contaminant sources with 45% accuracy, which was comparable to the results seen with a combination of five genetic markers (icaA, IS256, sesD [bhp], mecA, and arginine catabolic mobile element [ACME]). Thus, analysis of population structure with subgenomic data shows the distinction of hospital and nonhospital sources and the near-inseparability of sources within a hospital.
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Affiliation(s)
- Isaiah Tolo
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | | | - Rebecca S B Fischer
- Center for Infectious Disease, University of Texas Health Science Center, Houston, Texas, USA
| | - Eric L Brown
- Center for Infectious Disease, University of Texas Health Science Center, Houston, Texas, USA
| | - Barry M Gray
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
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Significance of Staphylococcus epidermidis in Health Care-Associated Infections, from Contaminant to Clinically Relevant Pathogen: This Is a Wake-Up Call! J Clin Microbiol 2016; 54:1679-1681. [PMID: 27170016 DOI: 10.1128/jcm.00743-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Coagulase-negative staphylococci, particularly Staphylococcus epidermidis, have been recognized as an important cause of health care-associated infections. Concurrently, S. epidermidis is a common contaminant in clinical cultures, which poses a diagnostic challenge. An article in this issue of Journal of Clinical Microbiology (I. Tolo, J. C. Thomas, R. S. B. Fischer, E. L. Brown, B. M. Gray, and D. A. Robinson, J Clin Microbiol 54:1711-1719, 2015, http://dx.doi.org/10.1128/JCM.03345-15) describes a rapid single nucleotide polymorphism-based assay for distinguishing between S. epidermidis isolates from hospital and nonhospital sources, which represents an important contribution to the characterization and understanding of S. epidermidis health care-associated infections.
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Deplano A, Vandendriessche S, Nonhoff C, Dodémont M, Roisin S, Denis O. National surveillance ofStaphylococcus epidermidisrecovered from bloodstream infections in Belgian hospitals. J Antimicrob Chemother 2016; 71:1815-9. [DOI: 10.1093/jac/dkw086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/28/2016] [Indexed: 01/18/2023] Open
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Kleinschmidt S, Huygens F, Faoagali J, Rathnayake IU, Hafner LM. Staphylococcus epidermidis as a cause of bacteremia. Future Microbiol 2015; 10:1859-79. [DOI: 10.2217/fmb.15.98] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus epidermidis is a biofilm-producing commensal organism found ubiquitously on human skin and mucous membranes, as well as on animals and in the environment. Biofilm formation enables this organism to evade the host immune system. Colonization of percutaneous devices or implanted medical devices allows bacteria access to the bloodstream. Isolation of this organism from blood cultures may represent either contamination during the blood collection procedure or true bacteremia. S. epidermidis bloodstream infections may be indolent compared with other bacteria. Isolation of S. epidermidis from a blood culture may present a management quandary for clinicians. Over-treatment may lead to patient harm and increases in healthcare costs. There are numerous reports indicating the difficulty of predicting clinical infection in patients with positive blood cultures with this organism. No reliable phenotypic or genotypic algorithms currently exist to predict the pathogenicity of a S. epidermidis bloodstream infection. This review will discuss the latest advances in identification methods, global population structure, pathogenicity, biofilm formation, antimicrobial resistance and clinical significance of the detection of S. epidermidis in blood cultures. Previous studies that have attempted to discriminate between invasive and contaminating strains of S. epidermidis in blood cultures will be analyzed.
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Affiliation(s)
- Sharon Kleinschmidt
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Microbiology Department, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Flavia Huygens
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Joan Faoagali
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Louise M Hafner
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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Long-term molecular epidemiology of Staphylococcus epidermidis blood culture isolates from patients with hematological malignancies. PLoS One 2014; 9:e99045. [PMID: 24896826 PMCID: PMC4045895 DOI: 10.1371/journal.pone.0099045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 05/10/2014] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus epidermidis is an important cause of bloodstream infections in patients with hematological malignancies. Knowledge of the long-term epidemiology of these infections is limited. We surveyed all S. epidermidis blood culture isolates from patients treated for hematological malignancies at the University Hospital of Örebro, Sweden from 1980 to 2009. A total of 373 S. epidermidis isolates were identified and multilocus sequence typing, staphylococcal chromosome cassette mec (SCCmec) typing and standard antibiotic susceptibility testing were employed to characterize these isolates. The majority of the isolates 361/373 (97%) belonged to clonal complex 2, and the 373 isolates were divided into 45 sequence types (STs); Simpson's Diversity Index was 0.56. The most prevalent STs were ST2 (243/373, 65%) and ST215 (28/373, 8%). Ninety three percent (226/243) of the ST2 isolates displayed either SCCmec type III or IV. ST2 and 215 were isolated during the entire study period, and together these STs caused temporal peaks in the number of positive blood cultures of S. epidermidis. Methicillin resistance was detected in 213/273 (78%) of all isolates. In the two predominating STs, ST2 and ST215, methicillin resistance was detected in 256/271 isolates (95%), compared with 34/100 (34%) in other STs (p<0.001). In conclusion, in this long-term study of patients with hematological malignancies, we demonstrate a predominance of methicillin-resistant ST2 among S. epidermidis blood culture isolates.
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Heterogeneous glycopeptide intermediate Staphylococcus epidermidis isolated from prosthetic joint infections. Eur J Clin Microbiol Infect Dis 2013; 33:911-7. [DOI: 10.1007/s10096-013-2025-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
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Differing lifestyles of Staphylococcus epidermidis as revealed through Bayesian clustering of multilocus sequence types. INFECTION GENETICS AND EVOLUTION 2013; 22:257-64. [PMID: 23816539 DOI: 10.1016/j.meegid.2013.06.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/11/2013] [Accepted: 06/19/2013] [Indexed: 11/23/2022]
Abstract
Staphylococcus epidermidis is part of the normal bacterial flora of human skin and a leading cause of infections associated with indwelling medical devices. Previous phylogenetic analyses of subgenomic data have been unable to distinguish between S. epidermidis strains with nosocomial or commensal lifestyles, despite the identification of specific phenotypes and accessory genes that may contribute to such lifestyles. To attempt to better define the population structure of this species, the international S. epidermidis multilocus sequence typing database was analyzed with the Bayesian clustering programs STRUCTURE and BAPS. A total of six genetic clusters (GCs) were identified. A local population of S. epidermidis from clinical specimens was classified according to these six GCs, and further characterized for antibiotic susceptibilities, biofilm, and various genetic markers. GC5 was abundant and significantly enriched for isolates that were resistant to four classes of antibiotics, high biofilm production, and positive for the virulence markers icaA, IS256, and sesD/bhp, indicating its potential clinical relevance. In contrast, GC2 was rare and contained the only isolates positive for the putative commensal marker, fdh. GC1 and GC6 were abundant but not significantly associated with any of the examined characteristics, except for sesF/aap and GC6. GC3 was rare and identified as a potential genetic sink that received, but did not donate, core genetic material from other GCs. In conclusion, population genetics analyses were essential for identifying clusters of strains that may differ in their adaptation to nosocomial or commensal lifestyles. These results provide a new, population genetics framework for studying S. epidermidis.
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Molecular analysis of Staphylococcus epidermidis strains isolated from community and hospital environments in China. PLoS One 2013; 8:e62742. [PMID: 23675424 PMCID: PMC3652868 DOI: 10.1371/journal.pone.0062742] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/25/2013] [Indexed: 11/19/2022] Open
Abstract
Background Staphylococcus epidermidis is a common cause of nosocomial infections worldwide. This study analyzed the differences in genetic endowment and clonal lineages with pathogenesis and resistance traits of S. epidermidis isolates collected from community and hospital environments (patients and healthcare staff) of the same ecological niche, time period, and geographical location in China. Methodology/Principal Findings Molecular epidemiology and population analysis showed that nasal colonization rates of S. epidermidis in the community of Shanghai area of China and in healthcare personnel were 44.8% (methicillin-resistant S. epidermidis, MRSE: 17.2%) and 61.3% (MRSE: 30.0%), respectively. 86.7% of clinical isolates were MRSE. Among the strains studied, 44 sequence types (STs) were identified with 91.7% belonging to clonal complex 2 (CC2). Only 40.8% isolates from patients were also found in healthy individuals. MRSE-ST2-SCCmecIII was the predominant clone in clinical isolates, almost resistant to all antibiotics tested. Biofilm-related genes IS256 and icaA were detected in majority of the predominant clinical MRSE-ST2 clone with a 40.5% biofilm-positive rate. No ST2 isolate was found in community setting. We found a high prevalence of arginine catabolic mobile element (ACME) (74.1%). The prevalence of ACME-arc and ACME-opp3 clusters was 71.6% and 32.4%, respectively. Methicillin-sensitive S. epidermidis (MSSE) isolates harbored more ACME (83.3%) than MRSE isolates (67.7%), and there was no association between ACME and SCCmec types. An association was found between low-level ACME presence and invasive infections. Conclusions/Significance We observed a high level of diversity within S. epidermidis in this study, with CC2 as the dominant clonal complex in both community and hospital settings. Only 40.8% of the isolates from patients were also found in healthy individuals. Contrary to that biofilm formation and multiple antibiotic resistance were associated closely with pathogenicity of S. epidermidis, ACME was more likely to be an indicator for colonization rather than a virulence factor.
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Campanile F, Mongelli G, Bongiorno D, Adembri C, Ballardini M, Falcone M, Menichetti F, Repetto A, Sabia C, Sartor A, Scarparo C, Tascini C, Venditti M, Zoppi F, Stefani S. Worrisome trend of new multiple mechanisms of linezolid resistance in staphylococcal clones diffused in Italy. J Clin Microbiol 2013; 51:1256-9. [PMID: 23345292 PMCID: PMC3666802 DOI: 10.1128/jcm.00098-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 01/14/2013] [Indexed: 01/03/2023] Open
Abstract
In order to assess the frequency of clinically relevant linezolid-resistant staphylococcal isolates, and the role of linezolid in maintaining and coselecting multiple resistance mechanisms (cfr, 23S rRNA, L3/L4 mutations), a prospective Italian study was performed from 2010 to 2011 to confirm the diffusion of three major multidrug-resistant clones (ST2, ST5, ST23).
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Affiliation(s)
| | | | | | - Chiara Adembri
- Azienda Ospedaliera Universitaria Careggi, Firenze, Italy
| | | | | | | | | | - Carla Sabia
- University of Modena and Reggio, Modena, Italy
| | - Assunta Sartor
- Santa Maria della Misericordia University Hospital, Udine, Italy
| | - Claudio Scarparo
- Santa Maria della Misericordia University Hospital, Udine, Italy
| | | | | | - Federica Zoppi
- Azienda Ospedaliera Universitaria Careggi, Firenze, Italy
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Comparative epidemiology of Staphylococcus epidermidis isolates from patients with catheter-related bacteremia and from healthy volunteers. J Clin Microbiol 2013; 51:1541-7. [PMID: 23486718 DOI: 10.1128/jcm.03378-12] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus epidermidis is a major cause of catheter-related bloodstream infections (CRBSIs). Recent studies suggested the existence of well-adapted, highly resistant, hospital-associated S. epidermidis clones. The molecular epidemiology of S. epidermidis in Belgian hospitals and the Belgian community has not been explored yet. We compared a set of 33 S. epidermidis isolates causing CRBSI in hospitalized patients with a set of 33 commensal S. epidermidis isolates. The factors analyzed included resistance to antibiotics and genetic diversity as determined by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and SCCmec typing. Additionally, the presence of virulence-associated mobile genetic elements, the ica operon and the arginine catabolic mobile element (ACME), was assessed and compared against clinical data. CRBSI S. epidermidis isolates were significantly resistant to more antibiotics than commensal S. epidermidis isolates. The two populations studied were very diverse and genetically distinct as only 23% of the 37 PFGE types observed were harbored by both CRBSI and commensal isolates. ACME was found in 76% of S. epidermidis strains, regardless of their origin, while the ica operon was significantly more prevalent in CRBSI isolates than in commensal isolates (P < 0.05). Nine patients presented a clinically severe CRBSI, eight cases of which were due to an ica-positive multiresistant isolate belonging to sequence type 2 (ST2) or ST54. S. epidermidis isolates causing CRBSI were more resistant and more often ica positive than commensal S. epidermidis isolates, which were genetically heterogeneous and susceptible to the majority of antibiotics tested. Clinically severe CRBSIs were due to isolates belonging to two closely related MLST types, ST2 and ST54.
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Kern A, Perreten V. Clinical and molecular features of methicillin-resistant, coagulase-negative staphylococci of pets and horses. J Antimicrob Chemother 2013; 68:1256-66. [DOI: 10.1093/jac/dkt020] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Genetic analysis of glycopeptide-resistant Staphylococcus epidermidis strains from bone and joint infections. J Clin Microbiol 2012; 51:1014-9. [PMID: 23269734 DOI: 10.1128/jcm.02608-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycopeptide-resistant Staphylococcus epidermidis (GRSE) strains are of increasing concern in bone and joint infections (BJIs). Using multilocus sequence typing and multilocus variable-number tandem repeat analysis, we show that BJI-associated GRSE strains are genetically diverse but arise from related, multiresistant hospital sequence types (STs), mostly ST2, ST5, and ST23.
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