1
|
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.
Collapse
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
| |
Collapse
|
2
|
Lee DH, Lee K, Kim YS, Cha CJ. Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis. mSystems 2024; 9:e0022624. [PMID: 38727238 PMCID: PMC11237394 DOI: 10.1128/msystems.00226-24] [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: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis. IMPORTANCE A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.
Collapse
Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| |
Collapse
|
3
|
Simon SJ, Sater M, Herriott I, Huntley M, Briars E, Hollenbeck BL. Staphylococcus epidermidis joint isolates: Whole-genome sequencing demonstrates evidence of hospital transmission and common antimicrobial resistance. Infect Control Hosp Epidemiol 2024; 45:150-156. [PMID: 38099465 DOI: 10.1017/ice.2023.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
OBJECTIVE We investigated genetic, epidemiologic, and environmental factors contributing to positive Staphylococcus epidermidis joint cultures. DESIGN Retrospective cohort study with whole-genome sequencing (WGS). PATIENTS We identified S. epidermidis isolates from hip or knee cultures in patients with 1 or more prior corresponding intra-articular procedure at our hospital. METHODS WGS and single-nucleotide polymorphism-based clonality analyses were performed, including species identification, in silico multilocus sequence typing (MLST), phylogenomic analysis, and genotypic assessment of the prevalence of specific antibiotic resistance and virulence genes. Epidemiologic review was performed to compare cluster and noncluster cases. RESULTS In total, 60 phenotypically distinct S. epidermidis isolates were identified. After removal of duplicates and impure samples, 48 isolates were used for the phylogenomic analysis, and 45 (93.7%) isolates were included in the clonality analysis. Notably, 5 S. epidermidis strains (10.4%) showed phenotypic susceptibility to oxacillin yet harbored mecA, and 3 (6.2%) strains showed phenotypic resistance despite not having mecA. Smr was found in all isolates, and mupA positivity was not observed. We also identified 6 clonal clusters from the clonality analysis, which accounted for 14 (31.1%) of the 45 S. epidermidis isolates. Our epidemiologic investigation revealed ties to common aspirations or operative procedures, although no specific common source was identified. CONCLUSIONS Most S. epidermidis isolates from clinical joint samples are diverse in origin, but we identified an important subset of 31.1% that belonged to subclinical healthcare-associated clusters. Clusters appeared to resolve spontaneously over time, suggesting the benefit of routine hospital infection control and disinfection practices.
Collapse
Affiliation(s)
- Samantha J Simon
- Research Department, New England Baptist Hospital, Boston, Massachusetts
| | | | | | | | | | - Brian L Hollenbeck
- Research Department, New England Baptist Hospital, Boston, Massachusetts
- Infectious Diseases, New England Baptist Hospital, Boston, Massachusetts
| |
Collapse
|
4
|
Gómez-Alonso IS, Betanzos-Cabrera G, Moreno-Lafont MC, Cancino-Diaz ME, García-Pérez BE, Cancino-Diaz JC. Non-biofilm-forming Staphylococcus epidermidis planktonic cell supernatant induces alterations in osteoblast biological function. Sci Rep 2024; 14:1807. [PMID: 38245549 PMCID: PMC10799936 DOI: 10.1038/s41598-024-51899-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
Staphylococcal biofilms significantly contribute to prosthetic joint infection (PJI). However, 40% of S. epidermidis PJI isolates do not produce biofilms, which does not explain the role of biofilms in these cases. We studied whether the supernatant from planktonic S. epidermidis alters osteoblast function. Non-biofilm-forming S. epidermidis supernatants (PJI- clinical isolate, healthy skin isolate (HS), and ATCC12228 reference strain) and biofilm-forming supernatants (PJI+ clinical isolate, ATCC35984 reference strain, and Staphylococcus aureus USA300 reference strain) were included. Osteoblasts stimulated with supernatants from non-biofilm-forming isolates for 3, 7, and 14 days showed significantly reduced cellular DNA content compared with unstimulated osteoblasts, and apoptosis was induced in these osteoblasts. Similar results were obtained for biofilm-forming isolates, but with a greater reduction in DNA content and higher apoptosis. Alkaline phosphatase activity and mineralization were significantly reduced in osteoblasts treated with supernatants from non-biofilm-forming isolates compared to the control at the same time points. However, the supernatants from biofilm-forming isolates had a greater effect than those from non-biofilm-forming isolates. A significant decrease in the expression of ATF4, RUNX2, ALP, SPARC, and BGLAP, and a significant increase in RANK-L expression were observed in osteoblasts treated with both supernatants. These results demonstrate that the supernatants of the S. epidermidis isolate from the PJI- and HS (commensal) with a non-biofilm-forming phenotype alter the function of osteoblasts (apoptosis induction, failure of cell differentiation, activation of osteoblasts, and induction of bone resorption), similar to biofilm-forming isolates (PJI+, ATCC35984, and S. aureus USA300), suggesting that biofilm status contributes to impaired osteoblast function and that the planktonic state can do so independently of biofilm production.
Collapse
Affiliation(s)
- Itzia Sidney Gómez-Alonso
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, 11350, Mexico City, Mexico
| | - Gabriel Betanzos-Cabrera
- Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Actopan Camino a Tilcuautla S/N., Pueblo San Juan Tilcuautla, 42160, Pachuca Hidalgo, Mexico
| | - Martha Cecilia Moreno-Lafont
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, 11350, Mexico City, Mexico
| | - Mario Eugenio Cancino-Diaz
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, 11350, Mexico City, Mexico
| | - Blanca Estela García-Pérez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, 11350, Mexico City, Mexico
| | - Juan Carlos Cancino-Diaz
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, 11350, Mexico City, Mexico.
| |
Collapse
|
5
|
Abedi AA, Varnum C, Pedersen AB, Gromov K, Hallas J, Iversen P, Jakobsen T, Jimenez-Solem E, Kidholm K, Kjerulf A, Lange J, Odgaard A, Rosenvinge FS, Solgaard S, Sperling K, Stegger M, Christensen R, Overgaard S. Effect of single versus multiple prophylactic antibiotic doses on prosthetic joint infections following primary total hip arthroplasty in patients with osteoarthritis at public and private hospitals in Denmark: protocol for a nationwide cross-over, cluster randomised, non-inferiority trial [The Pro-Hip-Quality Trial]. BMJ Open 2023; 13:e071487. [PMID: 37604637 PMCID: PMC10445366 DOI: 10.1136/bmjopen-2022-071487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/21/2023] [Indexed: 08/23/2023] Open
Abstract
INTRODUCTION A feared complication after total hip arthroplasty (THA) is prosthetic joint infection (PJI), associated with high morbidity and mortality. Prophylactic antibiotics can reduce the risk of PJI. However, there is no consensus on the dosages and current recommendations are based on a low evidence level. The objective is to compare the effect of a single versus multiple doses of prophylactic antibiotics administered within 24 hours on PJI. METHODS AND ANALYSIS The study is designed as a cross-over, cluster randomised, non-inferiority trial. All clinical centres use both antibiotic practices (1 year of each intervention). All Danish orthopaedic surgery departments will be involved: Based on quality databases, 2-year cohorts of approximately 20 000 primary THAs conducted at 39 public and private hospitals, will be included. INCLUSION CRITERIA age ≥18 years, all indications for THA except patients operated due to acute or sequelae from proximal femoral or pelvic fractures or bone tumour or metastasis. The primary outcome is PJI within 90 days after primary THA. Secondary outcomes include (1) serious adverse events, (2) potential PJI, (3) length of hospitalisation stay, (4) cardiovascular events, (5) hospital-treated infections, (6) community-based antibiotic use, (7) opioid use and (8) use of acetaminophen and non-steroidal anti-inflammatory drugs. All outcome measures will be extracted from national databases. Analyses will be based on the intention-to-treat population. Non-inferiority will be shown if the upper limit of the two-sided 95% CI for the OR is less than 1.32 for the single dose as compared with multiple doses. The results will establish best practice on antibiotic prophylaxis dosages in the future. ETHICS AND DISSEMINATION This study has been approved by Committees on Health Research Ethics for The Capital Region of Denmark (21069108) and The Danish Medicines Agency (2021091723). All results will be presented in peer-reviewed medical journals and international conferences. TRIAL REGISTRATION NUMBER NCT05530551.
Collapse
Affiliation(s)
- Armita Armina Abedi
- Department of Orthopedic Surgery and Traumatology, Copenhagen University Hospital Bispebjerg, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Claus Varnum
- Department of Orthopedics, Lillebaelt Hospital - University Hospital Southern Denmark, Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Alma Becic Pedersen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Kirill Gromov
- Department of Orthopedic Surgery, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Jesper Hallas
- Department of Public Health, Clinical Pharmacology, Pharmacy, and Environmental Medicine, University of Southern Denmark, Odense, Denmark
| | - Pernille Iversen
- The Danish Clinical Quality Program- National Clinical Registries (RKKP), Copenhagen, Denmark
| | - Thomas Jakobsen
- Department of Orthopedics, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Espen Jimenez-Solem
- Department of Clinical Pharmacology, Bispebjerg Hospital, Copenhagen, Denmark
| | - Kristian Kidholm
- Centre for Innovative Medical Technology, Odense Universitetshospital, Odense, Denmark
| | - Anne Kjerulf
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Jeppe Lange
- Department of Orthopedic Surgery, Regional Hospital Horsens, Horsens, Denmark
- Department of Clinical Medicine, Århus Universitet Klinisk Institut, Aarhus, Denmark
| | - Anders Odgaard
- Department of Orthopaedic Surgery, Rigshospitalet, Copenhagen, Denmark
| | | | - Søren Solgaard
- Department of Hip and Knee Surgery, Copenhagen University Hospital, Herlev-Gentofte University Hospital, Hellerup, Denmark
| | - Kim Sperling
- Department of Orthopedic Surgery, Nastved Hospital, Nastved, Denmark
| | - Marc Stegger
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Robin Christensen
- Parker Institute, Frederiksberg and Bispebjerg Hospital, Copenhagen, Denmark
| | - Søren Overgaard
- Department of Orthopedic Surgery and Traumatology, Copenhagen University Hospital Bispebjerg, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
| |
Collapse
|
6
|
Coustillères F, Renault V, Corvec S, Dupieux C, Simões PM, Lartigue MF, Plouzeau-Jayle C, Tande D, Lamoureux C, Lemarié C, Chenouard R, Laurent F, Lemaignen A, Bémer P. Clinical, Bacteriological, and Genetic Characterization of Bone and Joint Infections Involving Linezolid-Resistant Staphylococcus epidermidis: a Retrospective Multicenter Study in French Reference Centers. Microbiol Spectr 2023; 11:e0419022. [PMID: 37133395 PMCID: PMC10269892 DOI: 10.1128/spectrum.04190-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/09/2023] [Indexed: 05/04/2023] Open
Abstract
The choice of the best probabilistic postoperative antibiotics in bone and joint infections (BJIs) is still challenging. Since the implementation of protocolized postoperative linezolid in six French referral centers, linezolid-resistant multidrug-resistant Staphylococcus epidermidis (LR-MDRSE) strains were isolated in patients with BJI. We aimed here to describe clinical, microbiological, and molecular patterns associated with these strains. All patients with at least one intraoperative specimen positive for LR-MDRSE between 2015 and 2020 were included in this retrospective multicenter study. Clinical presentation, management, and outcome were described. LR-MDRSE strains were investigated by MIC determination for linezolid and other anti-MRSA antibiotics, characterization of genetic determinants of resistance, and phylogenetic analysis. Forty-six patients (colonization n = 10, infection n = 36) were included in five centers, 45 had prior exposure to linezolid, 33 had foreign devices. Clinical success was achieved for 26/36 patients. Incidence of LR-MDRSE increased over the study period. One hundred percent of the strains were resistant to oxazolidinones, gentamicin, clindamycin, ofloxacin, rifampicin, ceftaroline, and ceftobiprole, and susceptible to cyclins, daptomycin, and dalbavancin. Susceptibility to delafloxacin was bimodal. Molecular analysis was performed for 44 strains, and the main mutation conferring linezolid resistance was the 23S rRNA G2576T mutation. All strains belonged to the sequence type ST2 or its clonal complex, and phylogenetic analysis showed emergence of five populations corresponding geographically to the centers. We showed the emergence of new clonal populations of highly linezolid-resistant S. epidermidis in BJIs. Identifying patients at risk for LR-MDRSE acquisition and proposing alternatives to systematic postoperative linezolid use are essential. IMPORTANCE The manuscript describes the emergence of clonal linezolid-resistant strains of Staphylococcus epidermidis (LR-MDRSE) isolated from patients presenting with bone and joint infections. Incidence of LR-MDRSE increased over the study period. All strains were highly resistant to oxazolidinones, gentamicin, clindamycin, ofloxacin, rifampicin, ceftaroline, and ceftobiprole, but were susceptible to cyclins, daptomycin, and dalbavancin. Susceptibility to delafloxacin was bimodal. The main mutation conferring linezolid resistance was the 23S rRNA G2576T mutation. All strains belonged to the sequence type ST2 or its clonal complex, and phylogenetic analysis showed emergence of five populations corresponding geographically to the centers. LR-MDRSE bone and joint infections seem to be accompanied by an overall poor prognosis related to comorbidities and therapeutic issues. Identifying patients at risk for LR-MDRSE acquisition and proposing alternatives to systematic postoperative linezolid use become essential, with a preference for parenteral drugs such as lipopeptids or lipoglycopeptids.
Collapse
Affiliation(s)
- François Coustillères
- Service des Maladies Infectieuses, Centre Hospitalier Régional Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Tours, France
| | - Victor Renault
- Service de Bactériologie et des Contrôles microbiologiques, Hôtel-Dieu, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Nantes, France
| | - Stéphane Corvec
- Service de Bactériologie et des Contrôles microbiologiques, Hôtel-Dieu, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Nantes, France
| | - Céline Dupieux
- Hospices Civils de Lyon, Institut des Agents Infectieux, Service de Bactériologie, Centre National de Référence des Staphylocoques, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOAC Lyon), France
| | - Patricia Martins Simões
- Hospices Civils de Lyon, Institut des Agents Infectieux, Service de Bactériologie, Centre National de Référence des Staphylocoques, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOAC Lyon), France
| | - Marie Frédérique Lartigue
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Régional Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Tours, France
| | - Chloé Plouzeau-Jayle
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Poitiers, France
| | - Didier Tande
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Brest, France
| | - Claudie Lamoureux
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Brest, France
| | - Carole Lemarié
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Angers, France
| | - Rachel Chenouard
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Angers, France
| | - Frédéric Laurent
- Hospices Civils de Lyon, Institut des Agents Infectieux, Service de Bactériologie, Centre National de Référence des Staphylocoques, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOAC Lyon), France
| | - Adrien Lemaignen
- Service des Maladies Infectieuses, Centre Hospitalier Régional Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Tours, France
| | - Pascale Bémer
- Service de Bactériologie et des Contrôles microbiologiques, Hôtel-Dieu, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Nantes, France
| | - the CRIOGO (Centre de Référence des Infections Ostéo-articulaires du Grand Ouest) Study Team
- Service des Maladies Infectieuses, Centre Hospitalier Régional Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Tours, France
- Service de Bactériologie et des Contrôles microbiologiques, Hôtel-Dieu, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Nantes, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Service de Bactériologie, Centre National de Référence des Staphylocoques, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOAC Lyon), France
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Régional Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Tours, France
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Poitiers, France
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Brest, France
- Service de Bactériologie et d’Hygiène, Centre Hospitalier Universitaire, Centre Régional de Référence pour la prise en charge des IOA complexes (CRIOGO), Angers, France
| |
Collapse
|
7
|
Hellmann KT, Challagundla L, Gray BM, Robinson DA. Improved Genomic Prediction of Staphylococcus epidermidis Isolation Sources with a Novel Polygenic Score. J Clin Microbiol 2023; 61:e0141222. [PMID: 36840569 PMCID: PMC10035303 DOI: 10.1128/jcm.01412-22] [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: 09/23/2022] [Accepted: 01/22/2023] [Indexed: 02/25/2023] Open
Abstract
Staphylococcus epidermidis infections can be challenging to diagnose due to the species frequent contamination of clinical specimens and indolent course of infection. Nevertheless, S. epidermidis is the major cause of late-onset sepsis among premature infants and of intravascular infection in all age groups. Prior work has shown that bacterial virulence factors, antimicrobial resistances, and strains have up to 80% in-sample accuracy to distinguish hospital from community sources, but are unable to distinguish true bacteremia from blood culture contamination. Here, a phylogeny-informed genome-wide association study of 88 isolates was used to estimate effect sizes of particular genomic variants for isolation sources. A "polygenic score" was calculated for each isolate as the summed effect sizes of its repertoire of genomic variants. Predictive models of isolation sources based on polygenic scores were tested with in-samples and out-samples from prior studies of different patient populations. Polygenic scores from accessory genes (AGs) distinguished hospital from community sources with the highest accuracy to date, up to 98% for in-samples and 65% to 91% for various out-samples, whereas scores from single nucleotide polymorphisms (SNPs) had lower accuracy. Scores from AGs and SNPs achieved the highest in-sample accuracy to date, up to 76%, in distinguishing infection from contaminant sources within a hospital. Model training and testing data sets with more similar population structures resulted in more accurate predictions. This study reports the first use of a polygenic score for predicting a complex bacterial phenotype and shows the potential of this approach for enhancing S. epidermidis diagnosis.
Collapse
Affiliation(s)
- K. Taylor Hellmann
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Lavanya Challagundla
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Barry M. Gray
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi, USA
| |
Collapse
|
8
|
Löwbeer N, Stegger M, Söderquist B. Genomic characterization of beta-haemolytic streptococci isolated from prosthetic joint infections. APMIS 2023; 131:189-196. [PMID: 36715029 DOI: 10.1111/apm.13299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Prosthetic joint infection (PJI) is an increasing concern for the medical profession, as higher numbers of arthroplasty surgeries lead to rising PJI-related costs. Streptococcal PJIs constitute approximately 10% of PJIs, but their genetic features and characteristics remain largely unexplored. Little is known about antimicrobial resistance (AMR) rates, whether some sequence types (ST) dominate, and whether certain virulence-associated genes are overrepresented. We used whole-genome sequencing of Streptococcus dysgalactiae (n = 22), Streptococcus agalactiae (n = 10) and S. pyogenes (n = 1) to elicit genomic data on 33 beta-haemolytic streptococci isolated from PJIs in Region Örebro county, Sweden. Relatedness was inferred based on single nucleotide polymorphisms in S. dysgalactiae and S. agalactiae. The genomic data were screened for virulence-associated genes available in the Virulence Factor Database. All isolates were screened for both phenotypic and genotypic resistance. The S. dysgalactiae and S. agalactiae isolates were genetically diverse, although 32% of S. dysgalactiae isolates (n = 7) were ST20. The speS and PI-2A genes were less represented in these isolates among virulence-associated genes, and AMR was more frequently observed in S. agalactiae. We conclude that PJIs caused by beta-haemolytic streptococci are not dominated by genetically similar beta-haemolytic streptococci. There were distinct inter-species differences in AMR between S. agalactiae and S. dysgalactiae.
Collapse
Affiliation(s)
- Niklas Löwbeer
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marc Stegger
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| |
Collapse
|
9
|
Stamm J, Weißelberg S, Both A, Failla AV, Nordholt G, Büttner H, Linder S, Aepfelbacher M, Rohde H. Development of an artificial synovial fluid useful for studying Staphylococcus epidermidis joint infections. Front Cell Infect Microbiol 2022; 12:948151. [PMID: 35967857 PMCID: PMC9374174 DOI: 10.3389/fcimb.2022.948151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus epidermidis is a major causative agent of prosthetic joint infections (PJI). The ability to form biofilms supports this highly selective pathogenic potential. In vitro studies essentially relying on phenotypic assays and genetic approaches have provided a detailed picture of the molecular events contributing to biofilm assembly. A major limitation in these studies is the use of synthetic growth media, which significantly differs from the environmental conditions S. epidermidis encounters during host invasion. Building on evidence showing that growth in serum substantially affects S. epidermidis gene expression profiles and phenotypes, the major aim of this study was to develop and characterize a growth medium mimicking synovial fluid, thereby facilitating research addressing specific aspects related to PJI. Using fresh human plasma, a protocol was established allowing for the large-scale production of a medium that by biochemical analysis matches key characteristics of synovial fluid and therefore is referred to as artificial synovial fluid (ASF). By analysis of biofilm-positive, polysaccharide intercellular adhesion (PIA)-producing S. epidermidis 1457 and its isogenic, PIA- and biofilm-negative mutant 1457-M10, evidence is provided that the presence of ASF induces cluster formation in S. epidermidis 1457 and mutant 1457-M10. Consistent with the aggregative properties, both strains formed multilayered biofilms when analyzed by confocal laser scanning microscopy. In parallel to the phenotypic findings, expression analysis after growth in ASF found upregulation of genes encoding for intercellular adhesins (icaA, aap, and embp) as well as atlE, encoding for the major cell wall autolysin being responsible for eDNA release. In contrast, growth in ASF was associated with reduced expression of the master regulator agr. Collectively, these results indicate that ASF induces expression profiles that are able to support intercellular adhesion in both PIA-positive and PIA-negative S. epidermidis. Given the observation that ASF overall induced biofilm formation in a collection of S. epidermidis isolates from PJI, the results strongly support the idea of using growth media mimicking host environments. ASF may play an important role in future studies related to the pathogenesis of S. epidermidis PJI.
Collapse
Affiliation(s)
- Johanna Stamm
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Samira Weißelberg
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Anna Both
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | | | - Gerhard Nordholt
- Institute for Clinical Chemistry, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Büttner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Stefan Linder
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Martin Aepfelbacher
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
- Deutsches Zentrum für Infektionsmedizin, Standort Hamburg-Lübeck-Borstel, Hamburg, Germany
- *Correspondence: Holger Rohde,
| |
Collapse
|
10
|
Genomics of Staphylococcus aureus and Staphylococcus epidermidis from Periprosthetic Joint Infections and Correlation to Clinical Outcome. Microbiol Spectr 2022; 10:e0218121. [PMID: 35762769 PMCID: PMC9430453 DOI: 10.1128/spectrum.02181-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The approach of sequencing or genotyping to characterize the pathogenic potential of staphylococci from orthopedic device-related infection (ODRI) has been applied in recent studies. These studies described the genomic carriage of virulence in clinical strains and compared it with those in commensal strains. Only a few studies have directly correlated genomic profiles to patient outcome and phenotypic virulence properties in periprosthetic joint infections (PJIs). We investigated the association between genomic variations and virulence-associated phenotypes (biofilm-forming ability and antimicrobial resistance) in 111 staphylococcal strains isolated from patients with PJI and the infection outcome (resolved/unresolved). The presence of a strong biofilm phenotype in Staphylococcus aureus and an antibiotic-resistant phenotype in Staphylococcus epidermidis were both associated with treatment failure of PJI. In S. epidermidis, multidrug resistance (MDR) and resistance to rifampicin were associated with unresolved infection. Sequence type 45 (ST45) and ST2 were particularly enriched in S. aureus and S. epidermidis, respectively. S. epidermidis ST2 caused the majority of relapses and was associated with MDR and strong biofilm production, whereas ST215 correlated with MDR and non/weak biofilm production. S. aureusagr II correlated with resolved infection, while S. epidermidisagr I was associated with strong biofilm production and agr III with non/weak production. Collectively, our results highlight the importance of careful genomic and phenotypic characterization to anticipate the probability of the strain causing treatment failure in PJI. Due to the high rate of resistant S. epidermidis strains identified, this study provides evidence that the current recommended treatment of rifampicin and a fluoroquinolone should not be administered without knowledge of the resistance pattern. IMPORTANCE This study addresses the presence and frequency of particular genetic variants and virulence factors found in staphylococcal bacteria causing periprosthetic joint infection (PJI) of the hip and knee to ascertain their clinical relevance as predictors of treatment failure. We characterized the genetic virulence traits of a large collection of clinical staphylococci isolated from patients with PJI and evaluated their association with the patient’s infection outcome. The results showed that S. aureus strains that produced strong biofilms and S. epidermidis strains with resistance to several antibiotics associated significantly with unresolved infection. Some particular genetic variants associated with biofilm formation and multidrug resistance. These traits should be considered important risk factors for the diagnosis and treatment guidance in PJI.
Collapse
|
11
|
Altayb HN, Elbadawi HS, Baothman O, Kazmi I, Alzahrani FA, Nadeem MS, Hosawi S, Chaieb K. Whole-Genome Sequence of Multidrug-Resistant Methicillin-Resistant Staphylococcus epidermidis Carrying Biofilm-Associated Genes and a Unique Composite of SCCmec. Antibiotics (Basel) 2022; 11:antibiotics11070861. [PMID: 35884115 PMCID: PMC9312184 DOI: 10.3390/antibiotics11070861] [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: 05/16/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus epidermidis is part of the normal human flora that has recently become an important opportunistic pathogen causing nosocomial infections and tends to be multidrug-resistant. In this investigation, we aimed to study the genomic characteristics of methicillin-resistant S. epidermidis isolated from clinical specimens. Three isolates were identified using biochemical tests and evaluated for drug susceptibility. Genomic DNA sequences were obtained using Illumina, and were processed for analysis using various bioinformatics tools. The isolates showed multidrug resistance to most of the antibiotics tested in this study, and were identified with three types (III(3A), IV(2B&5), and VI(4B)) of the mobile genetic element SCCmec that carries the methicillin resistance gene (mecA) and its regulators (mecI and mecR1). A total of 11 antimicrobial resistance genes (ARGs) was identified as chromosomally mediated or in plasmids; these genes encode for proteins causing decreased susceptibility to methicillin (mecA), penicillin (blaZ), fusidic acid (fusB), fosfomycin (fosB), tetracycline (tet(K)), aminoglycosides (aadD, aac(6′)-aph(2′’)), fluoroquinolone (MFS antibiotic efflux pump), trimethoprim (dfrG), macrolide (msr(A)), and chlorhexidine (qacA)). Additionally, the 9SE strain belongs to the globally disseminated ST2, and harbors biofilm-formation genes (icaA, icaB, icaC, icaD, and IS256) with phenotypic biofilm production capability. It also harbors the fusidic acid resistance gene (fusB), which could increase the risk of device-associated healthcare infections, and 9SE has been identified as having a unique extra SCC gene (ccrB4); this new composite element of the ccr type needs more focus to better understand its role in the drug resistance mechanism.
Collapse
Affiliation(s)
- Hisham N. Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (O.B.); (I.K.); (F.A.A.); (M.S.N.); (S.H.); (K.C.)
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: ; Tel.: +966-549087515
| | - Hana S. Elbadawi
- Microbiology and Parasitology Department, Soba University Hospital, University of Khartoum, Khartoum 11115, Sudan;
| | - Othman Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (O.B.); (I.K.); (F.A.A.); (M.S.N.); (S.H.); (K.C.)
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (O.B.); (I.K.); (F.A.A.); (M.S.N.); (S.H.); (K.C.)
| | - Faisal A. Alzahrani
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (O.B.); (I.K.); (F.A.A.); (M.S.N.); (S.H.); (K.C.)
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (O.B.); (I.K.); (F.A.A.); (M.S.N.); (S.H.); (K.C.)
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (O.B.); (I.K.); (F.A.A.); (M.S.N.); (S.H.); (K.C.)
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (O.B.); (I.K.); (F.A.A.); (M.S.N.); (S.H.); (K.C.)
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environmental and Products, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| |
Collapse
|
12
|
Morales-Laverde L, Echeverz M, Trobos M, Solano C, Lasa I. Experimental Polymorphism Survey in Intergenic Regions of the icaADBCR Locus in Staphylococcus aureus Isolates from Periprosthetic Joint Infections. Microorganisms 2022; 10:microorganisms10030600. [PMID: 35336176 PMCID: PMC8955882 DOI: 10.3390/microorganisms10030600] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus is a leading cause of prosthetic joint infections (PJI) characterized by bacterial biofilm formation and recalcitrance to immune-mediated clearance and antibiotics. The molecular events behind PJI infection are yet to be unraveled. In this sense, identification of polymorphisms in bacterial genomes may help to establish associations between sequence variants and the ability of S. aureus to cause PJI. Here, we report an experimental nucleotide-level survey specifically aimed at the intergenic regions (IGRs) of the icaADBCR locus, which is responsible for the synthesis of the biofilm exopolysaccharide PIA/PNAG, in a collection of strains sampled from PJI and wounds. IGRs of the icaADBCR locus were highly conserved and no PJI-specific SNPs were found. Moreover, polymorphisms in these IGRs did not significantly affect transcription of the icaADBC operon under in vitro laboratory conditions. In contrast, an SNP within the icaR coding region, resulting in a V176E change in the transcriptional repressor IcaR, led to a significant increase in icaADBC operon transcription and PIA/PNAG production and a reduction in S. aureus virulence in a Galleria mellonella infection model. In conclusion, SNPs in icaADBCR IGRs of S. aureus isolates from PJI are not associated with icaADBC expression, PIA/PNAG production and adaptation to PJI.
Collapse
Affiliation(s)
- Liliana Morales-Laverde
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain; (L.M.-L.); (M.E.); (C.S.)
| | - Maite Echeverz
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain; (L.M.-L.); (M.E.); (C.S.)
| | - Margarita Trobos
- Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, 40530 Gothenburg, Sweden;
| | - Cristina Solano
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain; (L.M.-L.); (M.E.); (C.S.)
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain; (L.M.-L.); (M.E.); (C.S.)
- Correspondence:
| |
Collapse
|
13
|
Look Who's Talking: Host and Pathogen Drivers of Staphylococcus epidermidis Virulence in Neonatal Sepsis. Int J Mol Sci 2022; 23:ijms23020860. [PMID: 35055041 PMCID: PMC8775791 DOI: 10.3390/ijms23020860] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
Preterm infants are at increased risk for invasive neonatal bacterial infections. S. epidermidis, a ubiquitous skin commensal, is a major cause of late-onset neonatal sepsis, particularly in high-resource settings. The vulnerability of preterm infants to serious bacterial infections is commonly attributed to their distinct and developing immune system. While developmentally immature immune defences play a large role in facilitating bacterial invasion, this fails to explain why only a subset of infants develop infections with low-virulence organisms when exposed to similar risk factors in the neonatal ICU. Experimental research has explored potential virulence mechanisms contributing to the pathogenic shift of commensal S. epidermidis strains. Furthermore, comparative genomics studies have yielded insights into the emergence and spread of nosocomial S. epidermidis strains, and their genetic and functional characteristics implicated in invasive disease in neonates. These studies have highlighted the multifactorial nature of S. epidermidis traits relating to pathogenicity and commensalism. In this review, we discuss the known host and pathogen drivers of S. epidermidis virulence in neonatal sepsis and provide future perspectives to close the gap in our understanding of S. epidermidis as a cause of neonatal morbidity and mortality.
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Månsson E, Tevell S, Nilsdotter-Augustinsson Å, Johannesen TB, Sundqvist M, Stegger M, Söderquist B. Methicillin-Resistant Staphylococcus epidermidis Lineages in the Nasal and Skin Microbiota of Patients Planned for Arthroplasty Surgery. Microorganisms 2021; 9:microorganisms9020265. [PMID: 33525409 PMCID: PMC7911009 DOI: 10.3390/microorganisms9020265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus epidermidis, ubiquitous in the human nasal and skin microbiota, is a common causative microorganism in prosthetic joint infections (PJIs). A high proportion of PJI isolates have been shown to harbor genetic traits associated with resistance to/tolerance of agents used for antimicrobial prophylaxis in joint arthroplasties. These traits were found within multidrug-resistant S. epidermidis (MDRSE) lineages of multiple genetic backgrounds. In this study, the aim was to study whether MDRSE lineages previously associated with PJIs are present in the nasal and skin microbiota of patients planned for arthroplasty surgery but before hospitalization. We cultured samples from nares, inguinal creases, and skin over the hip or knee (dependent on the planned procedure) taken two weeks (median) prior to admittance to the hospital for total joint arthroplasty from 66 patients on agar plates selecting for methicillin resistance. S. epidermidis colonies were identified and tested for the presence of mecA. Methicillin-resistant S. epidermidis (MRSE) were characterized by Illumina-based whole-genome sequencing. Using this method, we found that 30/66 (45%) of patients were colonized with MRSE at 1–3 body sites. A subset of patients, 10/66 (15%), were colonized with MDRSE lineages associated with PJIs. The qacA gene was identified in MRSE isolates from 19/30 (63%) of MRSE colonized patients, whereas genes associated with aminoglycoside resistance were less common, found in 11/30 (37%). We found that MDRSE lineages previously associated with PJIs were present in a subset of patients’ pre-admission microbiota, plausibly in low relative abundance, and may be selected for by the current prophylaxis regimen comprising whole-body cleansing with chlorhexidine-gluconate containing soap. To further lower the rate of S. epidermidis PJIs, the current prophylaxis may need to be modified, but it is important for possible perioperative MDRSE transmission events and specific risk factors for MDRSE PJIs to be investigated before reevaluating antimicrobial prophylaxis.
Collapse
Affiliation(s)
- Emeli Månsson
- School of Medical Sciencies, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (S.T.); (M.S.); (B.S.)
- Centre for Clinical Research, Region Västmanland—Uppsala University, Hospital of Västmanland, Västerås, SE-721 89 Västerås, Sweden
- Correspondence:
| | - Staffan Tevell
- School of Medical Sciencies, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (S.T.); (M.S.); (B.S.)
- Department of Infectious Diseases, Karlstad Hospital and Centre for Clinical Research and Education, County Council of Värmland, SE-651 82 Karlstad, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Department of Infectious Diseases, and Department of Clinical and Experimental Medicine, Linköping University, SE-60182 Norrköping, Sweden;
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark;
| | - Martin Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden;
| | - Marc Stegger
- School of Medical Sciencies, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (S.T.); (M.S.); (B.S.)
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark;
| | - Bo Söderquist
- School of Medical Sciencies, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (S.T.); (M.S.); (B.S.)
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden;
| |
Collapse
|
16
|
Rendboe AK, Johannesen TB, Ingham AC, Månsson E, Iversen S, Baig S, Edslev S, Jensen JS, Söderquist B, Andersen PS, Stegger M. The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection. BMC Microbiol 2020; 20:362. [PMID: 33243146 PMCID: PMC7691061 DOI: 10.1186/s12866-020-02041-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. Infections are often caused by multidrug-resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients' quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive. In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of S. epidermidis communities. RESULTS Based on an assessment of > 800 genes from the S. epidermidis core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico, and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of S. epidermidis. The approach was validated on isolates representing skin commensals and on genomic mock communities with a sensitivity of < 10 copies/μL. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the S. epidermidis populations. Additionally, the qPCR showed a high degree of variation in absolute abundance of S. epidermidis. CONCLUSIONS The Epidome method is designed for use on primary samples to obtain important information on S. epidermidis abundance and diversity beyond species-level to answer questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of S. epidermidis communities, population dynamics, and niche selection. Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in low-biomass samples such as skin samples.
Collapse
Affiliation(s)
- Amalie Katrine Rendboe
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Emeli Månsson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Centre for Clinical Research, Hospital of Västmanland, Region Västmanland - Uppsala University, Västerås, Sweden
| | - Søren Iversen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sharmin Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen Skov Jensen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| |
Collapse
|